HEADER PROTEIN FIBRIL 20-DEC-10 3Q2X TITLE STRUCTURE OF AN AMYLOID FORMING PEPTIDE NKGAII (RESIDUES 27-32) FROM TITLE 2 AMYLOID BETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NKGAII HEXAPEPTIDE SEGMENT (UNP RESIDUES 698-703); COMPND 5 SYNONYM: ABPP,APPI,APP,ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID COMPND 6 PRECURSOR PROTEIN,BETA-AMYLOID PRECURSOR PROTEIN,CEREBRAL VASCULAR COMPND 7 AMYLOID PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: NKGAII (RESIDUES 27-32) FROM HUMAN AMYLOID BETA, SOURCE 7 SYNTHESIZED KEYWDS AMYLOID PROTOFIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR A.B.SORIAGA,M.R.SAWAYA,D.EISENBERG REVDAT 4 21-FEB-24 3Q2X 1 REMARK REVDAT 3 13-SEP-17 3Q2X 1 COMPND SOURCE DBREF REVDAT 2 30-NOV-11 3Q2X 1 JRNL REVDAT 1 12-OCT-11 3Q2X 0 JRNL AUTH J.P.COLLETIER,A.LAGANOWSKY,M.LANDAU,M.ZHAO,A.B.SORIAGA, JRNL AUTH 2 L.GOLDSCHMIDT,D.FLOT,D.CASCIO,M.R.SAWAYA,D.EISENBERG JRNL TITL MOLECULAR BASIS FOR AMYLOID-BETA POLYMORPHISM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 16938 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21949245 JRNL DOI 10.1073/PNAS.1112600108 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.1_357 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 3 NUMBER OF REFLECTIONS : 656 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.820 REMARK 3 FREE R VALUE TEST SET COUNT : 71 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 0.0000 - 1.4506 0.89 585 71 0.2041 0.2589 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.60 REMARK 3 B_SOL : 80.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.44100 REMARK 3 B22 (A**2) : -3.62200 REMARK 3 B33 (A**2) : 2.01790 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.71360 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 42 REMARK 3 ANGLE : 1.869 55 REMARK 3 CHIRALITY : 0.093 7 REMARK 3 PLANARITY : 0.005 7 REMARK 3 DIHEDRAL : 7.450 16 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3Q2X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 671 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 13.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 2.4M SODIUM REMARK 280 MALONATE, 15% V/V GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 2.41900 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL UNIT IS A PAIR OF BETA SHEETS WITH THE SIDE REMARK 300 CHAINS INTERDIGITATING BETWEEN THE SHEETS. ONE SHEET IS CONSTRUCTED REMARK 300 FROM UNIT CELL TRANSLATIONS ALONG THE B DIRECTION (I.E. X,Y+1,Z; X, REMARK 300 Y+2,Z; X,Y+3,Z, ETC.). THE OTHER SHEET IS CONSTRUCTED FROM SYMMETRY REMARK 300 OPERATORS -X+1,Y+1/2,-Z+1; -X+1,Y+3/2,-Z+1; -X+1,Y+5/2,-Z+1, ETC. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 4.83800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 9.67600 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 2.41900 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 7.25700 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 12.09500 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 DBREF 3Q2X A 1 6 UNP P05067 A4_HUMAN 698 703 SEQRES 1 A 6 ASN LYS GLY ALA ILE ILE FORMUL 2 HOH *2(H2 O) CRYST1 15.074 4.838 24.016 90.00 95.56 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.066339 0.000000 0.006453 0.00000 SCALE2 0.000000 0.206697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041835 0.00000 ATOM 1 N ASN A 1 6.895 1.404 1.451 1.00 5.38 N ANISOU 1 N ASN A 1 407 1380 255 332 289 -1 N ATOM 2 CA ASN A 1 6.768 0.679 2.709 1.00 4.83 C ANISOU 2 CA ASN A 1 359 1271 204 441 200 -15 C ATOM 3 C ASN A 1 5.715 1.341 3.587 1.00 3.85 C ANISOU 3 C ASN A 1 310 1035 118 246 8 -57 C ATOM 4 O ASN A 1 5.591 2.565 3.595 1.00 3.39 O ANISOU 4 O ASN A 1 344 848 95 482 -47 -72 O ATOM 5 CB ASN A 1 8.114 0.619 3.450 1.00 4.93 C ANISOU 5 CB ASN A 1 517 1025 330 383 296 8 C ATOM 6 CG ASN A 1 9.089 -0.336 2.802 1.00 7.21 C ANISOU 6 CG ASN A 1 592 1704 445 -56 288 -176 C ATOM 7 OD1 ASN A 1 8.694 -1.167 1.985 1.00 9.33 O ANISOU 7 OD1 ASN A 1 708 2339 497 -46 431 -311 O ATOM 8 ND2 ASN A 1 10.370 -0.233 3.165 1.00 8.54 N ANISOU 8 ND2 ASN A 1 675 2082 489 -314 230 -198 N ATOM 9 N LYS A 2 4.945 0.526 4.303 1.00 1.08 N ANISOU 9 N LYS A 2 115 195 101 25 -25 129 N ATOM 10 CA LYS A 2 3.957 1.042 5.239 1.00 1.33 C ANISOU 10 CA LYS A 2 182 202 119 170 -33 31 C ATOM 11 C LYS A 2 4.131 0.336 6.550 1.00 1.85 C ANISOU 11 C LYS A 2 208 383 113 120 111 -66 C ATOM 12 O LYS A 2 4.304 -0.896 6.601 1.00 1.34 O ANISOU 12 O LYS A 2 330 15 165 71 233 50 O ATOM 13 CB LYS A 2 2.526 0.764 4.778 1.00 3.19 C ANISOU 13 CB LYS A 2 227 698 287 304 -157 18 C ATOM 14 CG LYS A 2 2.098 1.367 3.475 1.00 5.85 C ANISOU 14 CG LYS A 2 276 1529 420 365 -300 -87 C ATOM 15 CD LYS A 2 0.603 1.011 3.289 1.00 7.51 C ANISOU 15 CD LYS A 2 311 1988 556 342 -398 -181 C ATOM 16 CE LYS A 2 0.041 1.339 1.938 1.00 8.57 C ANISOU 16 CE LYS A 2 349 2230 677 341 -416 -340 C ATOM 17 NZ LYS A 2 -1.430 1.041 1.971 1.00 9.57 N ANISOU 17 NZ LYS A 2 380 2508 750 286 -464 -352 N ATOM 18 N GLY A 3 4.030 1.100 7.623 1.00 1.62 N ANISOU 18 N GLY A 3 262 285 66 115 128 26 N ATOM 19 CA GLY A 3 4.175 0.510 8.933 1.00 2.74 C ANISOU 19 CA GLY A 3 230 740 71 263 122 189 C ATOM 20 C GLY A 3 3.287 1.223 9.916 1.00 1.81 C ANISOU 20 C GLY A 3 33 582 75 137 49 208 C ATOM 21 O GLY A 3 3.141 2.447 9.885 1.00 1.35 O ANISOU 21 O GLY A 3 160 273 79 206 93 134 O ATOM 22 N ALA A 4 2.682 0.445 10.792 1.00 1.14 N ANISOU 22 N ALA A 4 3 367 64 -31 -13 153 N ATOM 23 CA ALA A 4 1.943 1.012 11.889 1.00 1.05 C ANISOU 23 CA ALA A 4 10 361 30 -41 -2 80 C ATOM 24 C ALA A 4 2.467 0.350 13.134 1.00 0.63 C ANISOU 24 C ALA A 4 44 162 35 -14 37 10 C ATOM 25 O ALA A 4 2.549 -0.873 13.197 1.00 0.91 O ANISOU 25 O ALA A 4 206 111 30 151 79 58 O ATOM 26 CB ALA A 4 0.453 0.740 11.715 1.00 2.59 C ANISOU 26 CB ALA A 4 67 880 36 239 37 113 C ATOM 27 N ILE A 5 2.872 1.170 14.100 1.00 1.13 N ANISOU 27 N ILE A 5 210 125 93 57 106 -37 N ATOM 28 CA ILE A 5 3.256 0.695 15.413 1.00 2.42 C ANISOU 28 CA ILE A 5 349 496 75 368 -29 -119 C ATOM 29 C ILE A 5 2.243 1.317 16.368 1.00 3.46 C ANISOU 29 C ILE A 5 679 501 136 487 8 -138 C ATOM 30 O ILE A 5 2.169 2.543 16.495 1.00 4.86 O ANISOU 30 O ILE A 5 1122 565 160 480 209 -119 O ATOM 31 CB ILE A 5 4.696 1.123 15.794 1.00 2.27 C ANISOU 31 CB ILE A 5 279 543 40 247 -54 -146 C ATOM 32 CG1 ILE A 5 5.725 0.508 14.837 1.00 3.67 C ANISOU 32 CG1 ILE A 5 295 1085 16 198 -69 -57 C ATOM 33 CG2 ILE A 5 5.016 0.651 17.191 1.00 3.11 C ANISOU 33 CG2 ILE A 5 303 854 27 -4 -42 -132 C ATOM 34 CD1 ILE A 5 5.773 1.126 13.443 1.00 4.90 C ANISOU 34 CD1 ILE A 5 268 1569 27 126 -80 25 C ATOM 35 N ILE A 6 1.437 0.477 17.005 0.89 2.28 N ANISOU 35 N ILE A 6 263 423 182 136 -37 -269 N ATOM 36 CA ILE A 6 0.323 0.965 17.811 0.89 4.89 C ANISOU 36 CA ILE A 6 430 1141 285 315 -125 -324 C ATOM 37 C ILE A 6 0.365 0.332 19.185 0.89 6.89 C ANISOU 37 C ILE A 6 747 1564 307 33 27 -517 C ATOM 38 O ILE A 6 0.965 -0.729 19.354 0.89 8.11 O ANISOU 38 O ILE A 6 997 1832 254 103 35 -239 O ATOM 39 CB ILE A 6 -1.039 0.606 17.157 0.89 8.73 C ANISOU 39 CB ILE A 6 428 2441 449 631 -215 -318 C ATOM 40 CG1 ILE A 6 -1.141 1.173 15.749 0.89 9.44 C ANISOU 40 CG1 ILE A 6 445 2602 539 956 -277 -271 C ATOM 41 CG2 ILE A 6 -2.188 1.108 17.999 0.89 11.07 C ANISOU 41 CG2 ILE A 6 458 3201 549 453 -204 -165 C ATOM 42 CD1 ILE A 6 -2.461 0.815 15.081 0.89 10.69 C ANISOU 42 CD1 ILE A 6 665 2782 615 1010 -252 -397 C ATOM 43 OXT ILE A 6 -0.201 0.856 20.143 0.89 9.51 O ANISOU 43 OXT ILE A 6 921 2290 404 -261 143 -481 O TER 44 ILE A 6 HETATM 45 O HOH A 7 9.306 1.322 -0.067 1.00 9.67 O ANISOU 45 O HOH A 7 2099 1146 429 173 -392 -290 O HETATM 46 O HOH A 8 4.236 1.231 0.491 1.00 13.08 O MASTER 200 0 0 0 0 0 0 6 45 1 0 1 END