HEADER DE NOVO PROTEIN 16-NOV-16 5TXD TITLE STRUCTURE OF AMYLOID-BETA DERIVED PEPTIDE - NKGAIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: Z; COMPND 4 FRAGMENT: 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: SYNTHESIZED KEYWDS PROTEIN FIBRIL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SANGWAN,M.R.SAWAYA,D.EISENBERG REVDAT 4 03-APR-24 5TXD 1 REMARK REVDAT 3 06-MAR-24 5TXD 1 COMPND REVDAT 2 10-OCT-18 5TXD 1 COMPND JRNL REVDAT 1 15-NOV-17 5TXD 0 JRNL AUTH T.D.DO,S.SANGWAN,N.E.C.DE ALMEIDA,A.I.ILITCHEV,M.GIAMMONA, JRNL AUTH 2 M.R.SAWAYA,S.K.BURATTO,D.S.EISENBERG,M.T.BOWERS JRNL TITL DISTAL AMYLOID BETA-PROTEIN FRAGMENTS TEMPLATE AMYLOID JRNL TITL 2 ASSEMBLY. JRNL REF PROTEIN SCI. V. 27 1181 2018 JRNL REFN ESSN 1469-896X JRNL PMID 29349888 JRNL DOI 10.1002/PRO.3375 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 3 NUMBER OF REFLECTIONS : 679 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.190 REMARK 3 FREE R VALUE TEST SET COUNT : 76 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.020 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 5TXD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1000224982. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 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) : 0.9791 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 679 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 26.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 6 RESIDUE ALANINE BETA STRAND REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 13.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 20% PEG 3350, 0.2M REMARK 280 POTASSIUM PHOSPHATE DIBASIC, PH 5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 14.70100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.41350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 14.70100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.41350 REMARK 290 SMTRY3 4 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 ASSEMBLY IS A PAIR OF BETA SHEETS 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z 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 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 4.82700 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 4.82700 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 14.70100 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 2.41350 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 14.70100 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 7.24050 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 14.70100 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 2.41350 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 14.70100 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 7.24050 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 Z 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TXH RELATED DB: PDB REMARK 900 RELATED ID: 5TXD RELATED DB: PDB DBREF 5TXD Z 1 6 UNP P05067 A4_HUMAN 698 703 SEQADV 5TXD PHE Z 6 UNP P05067 ILE 703 CONFLICT SEQRES 1 Z 6 ASN LYS GLY ALA ILE PHE HET PO4 Z 101 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *(H2 O) SITE 1 AC1 4 ASN Z 1 LYS Z 2 PHE Z 6 HOH Z 201 CRYST1 29.402 4.827 26.612 90.00 102.04 90.00 C 1 2 1 4 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 0.034011 0.000000 0.007252 0.00000 SCALE2 0.000000 0.207168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038422 0.00000 ATOM 1 N ASN Z 1 -8.220 -1.457 10.787 1.00 6.70 N ATOM 2 CA ASN Z 1 -8.014 -2.133 9.508 1.00 5.69 C ATOM 3 C ASN Z 1 -7.082 -1.378 8.586 1.00 5.45 C ATOM 4 O ASN Z 1 -7.073 -0.155 8.564 1.00 6.38 O ATOM 5 CB ASN Z 1 -9.351 -2.355 8.807 1.00 6.14 C ATOM 6 CG ASN Z 1 -10.323 -3.117 9.672 1.00 7.80 C ATOM 7 OD1 ASN Z 1 -9.932 -4.035 10.395 1.00 6.89 O ATOM 8 ND2 ASN Z 1 -11.585 -2.725 9.631 1.00 7.52 N ATOM 9 N LYS Z 2 -6.282 -2.121 7.836 1.00 5.68 N ATOM 10 CA LYS Z 2 -5.319 -1.526 6.921 1.00 4.15 C ATOM 11 C LYS Z 2 -5.261 -2.324 5.630 1.00 4.36 C ATOM 12 O LYS Z 2 -5.369 -3.543 5.651 1.00 4.55 O ATOM 13 CB LYS Z 2 -3.933 -1.459 7.562 1.00 3.95 C ATOM 14 CG LYS Z 2 -3.920 -0.865 8.960 1.00 7.21 C ATOM 15 CD LYS Z 2 -2.510 -0.817 9.525 1.00 7.88 C ATOM 16 CE LYS Z 2 -1.690 0.282 8.860 1.00 10.92 C ATOM 17 NZ LYS Z 2 -0.277 0.348 9.393 1.00 8.72 N ATOM 18 N GLY Z 3 -5.090 -1.641 4.504 1.00 3.36 N ATOM 19 CA GLY Z 3 -5.029 -2.326 3.229 1.00 3.35 C ATOM 20 C GLY Z 3 -4.323 -1.539 2.147 1.00 2.13 C ATOM 21 O GLY Z 3 -4.221 -0.316 2.214 1.00 2.67 O ATOM 22 N ALA Z 4 -3.844 -2.256 1.139 1.00 3.47 N ATOM 23 CA ALA Z 4 -3.235 -1.636 -0.024 1.00 3.48 C ATOM 24 C ALA Z 4 -3.736 -2.312 -1.273 1.00 3.96 C ATOM 25 O ALA Z 4 -3.857 -3.545 -1.307 1.00 5.79 O ATOM 26 CB ALA Z 4 -1.739 -1.725 0.035 1.00 3.48 C ATOM 27 N ILE Z 5 -4.040 -1.505 -2.282 1.00 3.15 N ATOM 28 CA ILE Z 5 -4.428 -2.020 -3.582 1.00 4.23 C ATOM 29 C ILE Z 5 -3.582 -1.317 -4.633 1.00 4.12 C ATOM 30 O ILE Z 5 -3.572 -0.087 -4.702 1.00 4.16 O ATOM 31 CB ILE Z 5 -5.922 -1.793 -3.888 1.00 3.32 C ATOM 32 CG1 ILE Z 5 -6.821 -2.525 -2.876 1.00 3.99 C ATOM 33 CG2 ILE Z 5 -6.222 -2.278 -5.297 1.00 4.17 C ATOM 34 CD1 ILE Z 5 -6.980 -1.853 -1.502 1.00 4.25 C ATOM 35 N PHE Z 6 -2.861 -2.087 -5.441 1.00 5.71 N ATOM 36 CA PHE Z 6 -1.945 -1.490 -6.412 1.00 5.44 C ATOM 37 C PHE Z 6 -1.594 -2.445 -7.538 1.00 7.01 C ATOM 38 O PHE Z 6 -2.291 -3.448 -7.718 1.00 8.03 O ATOM 39 CB PHE Z 6 -0.677 -1.016 -5.709 1.00 5.01 C ATOM 40 CG PHE Z 6 0.032 -2.090 -4.930 1.00 4.75 C ATOM 41 CD1 PHE Z 6 -0.414 -2.472 -3.670 1.00 4.10 C ATOM 42 CD2 PHE Z 6 1.176 -2.688 -5.439 1.00 4.64 C ATOM 43 CE1 PHE Z 6 0.245 -3.446 -2.948 1.00 3.78 C ATOM 44 CE2 PHE Z 6 1.849 -3.660 -4.720 1.00 4.00 C ATOM 45 CZ PHE Z 6 1.385 -4.043 -3.473 1.00 4.51 C ATOM 46 OXT PHE Z 6 -0.626 -2.232 -8.289 1.00 8.38 O TER 47 PHE Z 6 HETATM 48 P PO4 Z 101 -6.065 -0.390 13.382 1.00 29.08 P HETATM 49 O1 PO4 Z 101 -5.821 -0.923 11.991 1.00 15.35 O HETATM 50 O2 PO4 Z 101 -7.065 0.744 13.323 1.00 33.88 O HETATM 51 O3 PO4 Z 101 -6.650 -1.476 14.271 1.00 21.93 O HETATM 52 O4 PO4 Z 101 -4.759 0.128 13.933 1.00 28.21 O HETATM 53 O HOH Z 201 -9.437 1.786 13.134 1.00 20.96 O CONECT 48 49 50 51 52 CONECT 49 48 CONECT 50 48 CONECT 51 48 CONECT 52 48 MASTER 225 0 1 0 0 0 1 6 52 1 5 1 END