HEADER MEMBRANE PROTEIN, DE NOVO PROTEIN 24-JUN-14 4TUT TITLE STRUCTURE OF A PRION PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRION PEPTIDE: GLY-GLY-TYR-MET-LEU-GLY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS PRION PEPTIDE, MEMBRANE PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.YU,S.-J.LEE,V.YEE REVDAT 4 27-DEC-23 4TUT 1 REMARK REVDAT 3 22-NOV-17 4TUT 1 SOURCE JRNL REMARK REVDAT 2 01-JUL-15 4TUT 1 KEYWDS REVDAT 1 27-MAY-15 4TUT 0 JRNL AUTH L.YU,S.J.LEE,V.C.YEE JRNL TITL CRYSTAL STRUCTURES OF POLYMORPHIC PRION PROTEIN BETA 1 JRNL TITL 2 PEPTIDES REVEAL VARIABLE STERIC ZIPPER CONFORMATIONS. JRNL REF BIOCHEMISTRY V. 54 3640 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 25978088 JRNL DOI 10.1021/ACS.BIOCHEM.5B00425 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 71.5 REMARK 3 NUMBER OF REFLECTIONS : 1860 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.071 REMARK 3 R VALUE (WORKING SET) : 0.070 REMARK 3 FREE R VALUE : 0.098 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.300 REMARK 3 FREE R VALUE TEST SET COUNT : 80 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 - 0.8996 0.71 1780 80 0.0700 0.0980 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.030 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 6.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 1.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 2.50 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 : 0.007 41 REMARK 3 ANGLE : 1.365 53 REMARK 3 CHIRALITY : 0.058 4 REMARK 3 PLANARITY : 0.010 7 REMARK 3 DIHEDRAL : 6.074 14 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 4TUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.72932 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1862 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 71.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 32.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.06800 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.5, 1.3 M REMARK 280 SODIUM ACETATE, AND 25 % ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 4.86550 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: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UBY RELATED DB: PDB REMARK 900 RELATED ID: 4UBZ RELATED DB: PDB REMARK 900 RELATED ID: 4W5L RELATED DB: PDB REMARK 900 RELATED ID: 4W5M RELATED DB: PDB REMARK 900 RELATED ID: 4W5P RELATED DB: PDB REMARK 900 RELATED ID: 4W5Y RELATED DB: PDB REMARK 900 RELATED ID: 4W67 RELATED DB: PDB REMARK 900 RELATED ID: 4W71 RELATED DB: PDB REMARK 900 RELATED ID: 4WBU RELATED DB: PDB REMARK 900 RELATED ID: 4WBV RELATED DB: PDB DBREF 4TUT A 126 131 PDB 4TUT 4TUT 126 131 SEQRES 1 A 6 GLY GLY TYR MET LEU GLY FORMUL 2 HOH *5(H2 O) CRYST1 10.395 9.731 17.382 90.00 105.94 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 0.096200 0.000000 0.027469 0.00000 SCALE2 0.000000 0.102764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.059830 0.00000 ATOM 1 N GLY A 126 17.293 1.560 23.968 1.00 2.01 N ANISOU 1 N GLY A 126 313 224 226 -27 -143 -11 N ATOM 2 CA GLY A 126 16.849 0.827 22.791 1.00 1.95 C ANISOU 2 CA GLY A 126 291 224 226 -26 -149 -3 C ATOM 3 C GLY A 126 15.759 1.608 22.098 1.00 2.10 C ANISOU 3 C GLY A 126 309 224 265 -16 -149 -6 C ATOM 4 O GLY A 126 15.565 2.786 22.386 1.00 2.85 O ANISOU 4 O GLY A 126 453 279 352 3 -231 -37 O ATOM 5 N GLY A 127 15.042 0.968 21.186 1.00 1.73 N ANISOU 5 N GLY A 127 232 206 219 24 -133 -2 N ATOM 6 CA GLY A 127 14.034 1.688 20.438 1.00 1.89 C ANISOU 6 CA GLY A 127 261 210 247 17 -147 -14 C ATOM 7 C GLY A 127 13.225 0.763 19.570 1.00 1.67 C ANISOU 7 C GLY A 127 224 151 259 13 -65 -9 C ATOM 8 O GLY A 127 13.387 -0.455 19.626 1.00 1.89 O ANISOU 8 O GLY A 127 285 123 312 44 -68 -23 O ATOM 9 N TYR A 128 12.346 1.343 18.764 1.00 1.31 N ANISOU 9 N TYR A 128 142 137 219 -18 -46 -11 N ATOM 10 CA TYR A 128 11.429 0.542 17.964 1.00 1.33 C ANISOU 10 CA TYR A 128 144 142 220 3 -40 -7 C ATOM 11 C TYR A 128 10.906 1.404 16.824 1.00 1.35 C ANISOU 11 C TYR A 128 122 175 217 12 -35 15 C ATOM 12 O TYR A 128 10.959 2.642 16.877 1.00 1.38 O ANISOU 12 O TYR A 128 159 168 198 19 -44 1 O ATOM 13 CB TYR A 128 10.261 -0.015 18.826 1.00 1.46 C ANISOU 13 CB TYR A 128 183 131 241 5 3 22 C ATOM 14 CG TYR A 128 9.455 1.105 19.430 1.00 1.53 C ANISOU 14 CG TYR A 128 188 173 219 -31 20 56 C ATOM 15 CD1 TYR A 128 9.869 1.725 20.609 1.00 1.71 C ANISOU 15 CD1 TYR A 128 207 224 220 22 51 60 C ATOM 16 CD2 TYR A 128 8.325 1.603 18.782 1.00 1.82 C ANISOU 16 CD2 TYR A 128 210 233 250 19 30 45 C ATOM 17 CE1 TYR A 128 9.179 2.805 21.129 1.00 1.85 C ANISOU 17 CE1 TYR A 128 247 235 220 71 63 62 C ATOM 18 CE2 TYR A 128 7.628 2.681 19.297 1.00 2.07 C ANISOU 18 CE2 TYR A 128 265 266 253 71 45 39 C ATOM 19 CZ TYR A 128 8.063 3.280 20.464 1.00 2.25 C ANISOU 19 CZ TYR A 128 318 295 241 123 77 54 C ATOM 20 OH TYR A 128 7.374 4.361 20.943 1.00 2.82 O ANISOU 20 OH TYR A 128 427 387 257 199 88 -17 O ATOM 21 N MET A 129 10.393 0.725 15.804 1.00 1.48 N ANISOU 21 N MET A 129 163 204 194 4 -57 -17 N ATOM 22 CA MET A 129 9.886 1.367 14.602 1.00 1.42 C ANISOU 22 CA MET A 129 162 207 170 1 -40 -5 C ATOM 23 C MET A 129 8.529 0.778 14.227 1.00 1.41 C ANISOU 23 C MET A 129 168 178 190 -1 -22 0 C ATOM 24 O MET A 129 8.331 -0.445 14.303 1.00 1.48 O ANISOU 24 O MET A 129 191 145 225 -26 -49 -3 O ATOM 25 CB MET A 129 10.878 1.204 13.444 1.00 1.64 C ANISOU 25 CB MET A 129 188 264 169 22 30 -16 C ATOM 26 CG MET A 129 10.389 1.773 12.116 1.00 2.05 C ANISOU 26 CG MET A 129 252 321 207 -32 93 -37 C ATOM 27 SD MET A 129 11.651 1.731 10.822 1.00 2.53 S ANISOU 27 SD MET A 129 341 335 286 -67 148 -75 S ATOM 28 CE MET A 129 12.712 3.096 11.307 1.00 2.77 C ANISOU 28 CE MET A 129 340 395 317 -87 92 -58 C ATOM 29 N LEU A 130 7.616 1.675 13.845 1.00 1.31 N ANISOU 29 N LEU A 130 126 187 186 -6 -51 -11 N ATOM 30 CA LEU A 130 6.288 1.336 13.342 1.00 1.44 C ANISOU 30 CA LEU A 130 142 189 216 -25 -59 -9 C ATOM 31 C LEU A 130 6.201 1.705 11.865 1.00 1.51 C ANISOU 31 C LEU A 130 146 195 232 -24 -70 12 C ATOM 32 O LEU A 130 6.332 2.883 11.515 1.00 1.82 O ANISOU 32 O LEU A 130 247 189 257 -20 -79 51 O ATOM 33 CB LEU A 130 5.197 2.088 14.105 1.00 1.84 C ANISOU 33 CB LEU A 130 203 259 238 20 1 0 C ATOM 34 CG LEU A 130 5.200 2.010 15.632 1.00 2.34 C ANISOU 34 CG LEU A 130 291 311 288 33 88 -26 C ATOM 35 CD1 LEU A 130 4.039 2.827 16.150 1.00 2.68 C ANISOU 35 CD1 LEU A 130 333 359 328 12 137 0 C ATOM 36 CD2 LEU A 130 5.101 0.573 16.118 1.00 2.98 C ANISOU 36 CD2 LEU A 130 460 343 330 49 133 1 C ATOM 37 N GLY A 131 5.968 0.709 11.012 1.00 1.62 N ANISOU 37 N GLY A 131 167 237 210 -14 -60 9 N ATOM 38 CA GLY A 131 5.756 0.943 9.595 1.00 1.77 C ANISOU 38 CA GLY A 131 196 278 201 -14 -62 22 C ATOM 39 C GLY A 131 4.389 0.496 9.111 1.00 1.61 C ANISOU 39 C GLY A 131 189 201 222 -29 -53 22 C ATOM 40 O GLY A 131 3.739 -0.348 9.757 1.00 1.63 O ANISOU 40 O GLY A 131 175 197 248 -24 -18 56 O ATOM 41 OXT GLY A 131 3.958 0.976 8.049 1.00 2.06 O ANISOU 41 OXT GLY A 131 262 282 238 -47 -77 43 O TER 42 GLY A 131 HETATM 43 O HOH A 201 8.283 3.636 9.679 1.00 7.45 O ANISOU 43 O HOH A 201 539 1301 992 -259 9 436 O HETATM 44 O HOH A 202 14.752 1.268 25.186 1.00 9.38 O ANISOU 44 O HOH A 202 729 2009 828 -438 167 -559 O HETATM 45 O HOH A 203 17.268 -1.078 25.446 1.00 2.59 O ANISOU 45 O HOH A 203 357 213 414 -9 -97 24 O HETATM 46 O HOH A 204 12.656 4.005 23.452 1.00 12.32 O ANISOU 46 O HOH A 204 944 1896 1840 -592 -66 236 O HETATM 47 O HOH A 205 12.047 1.052 23.073 1.00 6.76 O ANISOU 47 O HOH A 205 937 1124 507 190 229 223 O MASTER 198 0 0 0 0 0 0 6 46 1 0 1 END