HEADER OXIDOREDUCTASE 13-DEC-10 3PYM TITLE STRUCTURE OF GAPDH 3 FROM S.CEREVISIAE AT 2.0 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GAPDH 3; COMPND 5 EC: 1.2.1.12 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS NAD(P)-BINDING ROSSMANN-FOLD DOMAIN, ALPHA AND BETA PROTEIN, KEYWDS 2 OXIDOREDUCTASE, GLYCOLYSIS, NAD EXPDTA X-RAY DIFFRACTION AUTHOR I.GARCIA-SAEZ,F.KOZIELSKI,D.JOB,C.BOSCHERON REVDAT 2 13-SEP-23 3PYM 1 REMARK LINK REVDAT 1 11-JAN-12 3PYM 0 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 52308 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 5273 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 44.6264 - 4.3023 0.99 4928 526 0.1475 0.1636 REMARK 3 2 4.3023 - 3.4152 1.00 4743 588 0.1478 0.1775 REMARK 3 3 3.4152 - 2.9836 1.00 4774 478 0.1549 0.1910 REMARK 3 4 2.9836 - 2.7109 1.00 4704 547 0.1393 0.1978 REMARK 3 5 2.7109 - 2.5166 1.00 4722 542 0.1387 0.1889 REMARK 3 6 2.5166 - 2.3682 1.00 4675 531 0.1543 0.2141 REMARK 3 7 2.3682 - 2.2496 0.99 4672 490 0.1487 0.2066 REMARK 3 8 2.2496 - 2.1517 0.99 4641 517 0.1426 0.1857 REMARK 3 9 2.1517 - 2.0689 0.99 4603 564 0.1460 0.2204 REMARK 3 10 2.0689 - 2.0000 0.98 4573 490 0.1509 0.2028 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.65 REMARK 3 K_SOL : 0.44 REMARK 3 B_SOL : 46.86 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 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) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.37260 REMARK 3 B22 (A**2) : -1.77820 REMARK 3 B33 (A**2) : -0.59440 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.014 5222 REMARK 3 ANGLE : 1.517 7098 REMARK 3 CHIRALITY : 0.093 833 REMARK 3 PLANARITY : 0.008 891 REMARK 3 DIHEDRAL : 14.227 1900 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:115) REMARK 3 ORIGIN FOR THE GROUP (A): 30.0661 26.8333 27.6998 REMARK 3 T TENSOR REMARK 3 T11: -0.0006 T22: 0.0390 REMARK 3 T33: -0.0172 T12: 0.0057 REMARK 3 T13: 0.0511 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 1.3165 L22: 0.6093 REMARK 3 L33: 0.3589 L12: -0.6438 REMARK 3 L13: -0.2755 L23: 0.2564 REMARK 3 S TENSOR REMARK 3 S11: -0.1881 S12: 0.0191 S13: 0.2071 REMARK 3 S21: 0.2121 S22: 0.1099 S23: -0.0868 REMARK 3 S31: 0.0134 S32: 0.0087 S33: -0.0868 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 116:232) REMARK 3 ORIGIN FOR THE GROUP (A): 46.0707 8.9071 28.6861 REMARK 3 T TENSOR REMARK 3 T11: 0.0869 T22: 0.0698 REMARK 3 T33: 0.0742 T12: -0.0318 REMARK 3 T13: 0.0456 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.1769 L22: 0.1064 REMARK 3 L33: 0.0518 L12: -0.0897 REMARK 3 L13: -0.0961 L23: 0.0317 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: -0.0456 S13: -0.0366 REMARK 3 S21: 0.1065 S22: -0.0123 S23: 0.0541 REMARK 3 S31: 0.0593 S32: 0.0043 S33: 0.0342 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 233:293) REMARK 3 ORIGIN FOR THE GROUP (A): 51.2599 7.4895 12.7995 REMARK 3 T TENSOR REMARK 3 T11: 0.0926 T22: 0.0965 REMARK 3 T33: 0.0576 T12: -0.0158 REMARK 3 T13: 0.0189 T23: -0.0331 REMARK 3 L TENSOR REMARK 3 L11: 0.1463 L22: 0.3948 REMARK 3 L33: 0.1717 L12: -0.1224 REMARK 3 L13: 0.0062 L23: 0.0515 REMARK 3 S TENSOR REMARK 3 S11: 0.0162 S12: 0.1172 S13: -0.0355 REMARK 3 S21: -0.0860 S22: -0.0709 S23: 0.0032 REMARK 3 S31: 0.0796 S32: -0.0339 S33: 0.0417 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 2:148) REMARK 3 ORIGIN FOR THE GROUP (A): 59.9823 36.6375 -6.5136 REMARK 3 T TENSOR REMARK 3 T11: 0.1063 T22: 0.1932 REMARK 3 T33: 0.0303 T12: -0.0642 REMARK 3 T13: 0.0202 T23: -0.0280 REMARK 3 L TENSOR REMARK 3 L11: 0.4948 L22: 1.0473 REMARK 3 L33: 0.3164 L12: 0.5494 REMARK 3 L13: 0.2963 L23: 0.5114 REMARK 3 S TENSOR REMARK 3 S11: -0.1743 S12: 0.3132 S13: -0.0509 REMARK 3 S21: -0.2122 S22: 0.2950 S23: -0.1011 REMARK 3 S31: -0.0714 S32: 0.1668 S33: -0.1053 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 149:218) REMARK 3 ORIGIN FOR THE GROUP (A): 64.6529 47.7741 14.5973 REMARK 3 T TENSOR REMARK 3 T11: 0.0806 T22: 0.0975 REMARK 3 T33: 0.1169 T12: 0.0109 REMARK 3 T13: 0.0216 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 0.1186 L22: 0.0754 REMARK 3 L33: 0.0974 L12: -0.0108 REMARK 3 L13: 0.0761 L23: -0.0764 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: 0.0840 S13: 0.0643 REMARK 3 S21: -0.0846 S22: -0.0677 S23: -0.0809 REMARK 3 S31: 0.0141 S32: 0.0568 S33: 0.0485 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 219:291) REMARK 3 ORIGIN FOR THE GROUP (A): 51.3490 52.7648 15.5165 REMARK 3 T TENSOR REMARK 3 T11: 0.0645 T22: 0.0766 REMARK 3 T33: 0.1658 T12: 0.0189 REMARK 3 T13: -0.0057 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.1218 L22: 0.3024 REMARK 3 L33: 0.1320 L12: 0.0973 REMARK 3 L13: 0.0961 L23: -0.0026 REMARK 3 S TENSOR REMARK 3 S11: -0.0333 S12: -0.0072 S13: 0.1369 REMARK 3 S21: -0.0783 S22: 0.0030 S23: 0.0658 REMARK 3 S31: -0.0157 S32: -0.0414 S33: 0.0292 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 3PYM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000062973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JAN-04 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9340 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52575 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.70 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.09100 REMARK 200 FOR THE DATA SET : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER (CCP4 SUPPORTED) REMARK 200 STARTING MODEL: PDB ENTRY 1GD1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10.5-15.5% PEG, 50MM NAAC, 1MM DTT, REMARK 280 1MM NAD, PH 7.0, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 48.34250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.34250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 60.91700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.52600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.91700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.52600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.34250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.91700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.52600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.34250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.91700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.52600 REMARK 290 SMTRY3 8 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -159.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 121.83400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 48.34250 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 355 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 368 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 500 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 572 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET B 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 584 O HOH B 586 1.92 REMARK 500 N GLY B 56 O HOH B 437 2.04 REMARK 500 O HOH A 427 O HOH A 498 2.10 REMARK 500 O HOH B 359 O HOH B 578 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 460 O HOH A 462 4555 2.07 REMARK 500 O HOH B 427 O HOH B 486 3655 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 9 51.39 -115.72 REMARK 500 ASP A 61 -162.21 -128.92 REMARK 500 PHE A 100 62.74 -119.46 REMARK 500 THR A 120 49.15 -89.72 REMARK 500 ASN A 134 21.30 -146.92 REMARK 500 ALA A 148 -152.47 60.40 REMARK 500 SER A 190 69.08 -153.84 REMARK 500 ASP A 193 83.41 -158.36 REMARK 500 THR A 199 114.94 -38.82 REMARK 500 PRO A 234 6.16 -69.01 REMARK 500 VAL A 238 131.84 85.42 REMARK 500 PRO B 84 45.22 -77.79 REMARK 500 PHE B 100 58.95 -114.33 REMARK 500 THR B 120 48.29 -90.01 REMARK 500 ASN B 134 21.01 -147.06 REMARK 500 ALA B 148 -147.71 59.81 REMARK 500 SER B 190 71.20 -153.67 REMARK 500 ASP B 193 80.80 -157.71 REMARK 500 VAL B 238 129.87 94.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 20 O REMARK 620 2 ARG B 23 O 90.3 REMARK 620 3 VAL B 26 O 102.7 85.8 REMARK 620 4 HOH B 519 O 112.6 156.1 82.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 333 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRY A 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 333 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRY B 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 504 DBREF 3PYM A 1 332 UNP P00359 G3P3_YEAST 1 332 DBREF 3PYM B 1 332 UNP P00359 G3P3_YEAST 1 332 SEQRES 1 A 332 MET VAL ARG VAL ALA ILE ASN GLY PHE GLY ARG ILE GLY SEQRES 2 A 332 ARG LEU VAL MET ARG ILE ALA LEU SER ARG PRO ASN VAL SEQRES 3 A 332 GLU VAL VAL ALA LEU ASN ASP PRO PHE ILE THR ASN ASP SEQRES 4 A 332 TYR ALA ALA TYR MET PHE LYS TYR ASP SER THR HIS GLY SEQRES 5 A 332 ARG TYR ALA GLY GLU VAL SER HIS ASP ASP LYS HIS ILE SEQRES 6 A 332 ILE VAL ASP GLY LYS LYS ILE ALA THR TYR GLN GLU ARG SEQRES 7 A 332 ASP PRO ALA ASN LEU PRO TRP GLY SER SER ASN VAL ASP SEQRES 8 A 332 ILE ALA ILE ASP SER THR GLY VAL PHE LYS GLU LEU ASP SEQRES 9 A 332 THR ALA GLN LYS HIS ILE ASP ALA GLY ALA LYS LYS VAL SEQRES 10 A 332 VAL ILE THR ALA PRO SER SER THR ALA PRO MET PHE VAL SEQRES 11 A 332 MET GLY VAL ASN GLU GLU LYS TYR THR SER ASP LEU LYS SEQRES 12 A 332 ILE VAL SER ASN ALA SER CYS THR THR ASN CYS LEU ALA SEQRES 13 A 332 PRO LEU ALA LYS VAL ILE ASN ASP ALA PHE GLY ILE GLU SEQRES 14 A 332 GLU GLY LEU MET THR THR VAL HIS SER LEU THR ALA THR SEQRES 15 A 332 GLN LYS THR VAL ASP GLY PRO SER HIS LYS ASP TRP ARG SEQRES 16 A 332 GLY GLY ARG THR ALA SER GLY ASN ILE ILE PRO SER SER SEQRES 17 A 332 THR GLY ALA ALA LYS ALA VAL GLY LYS VAL LEU PRO GLU SEQRES 18 A 332 LEU GLN GLY LYS LEU THR GLY MET ALA PHE ARG VAL PRO SEQRES 19 A 332 THR VAL ASP VAL SER VAL VAL ASP LEU THR VAL LYS LEU SEQRES 20 A 332 ASN LYS GLU THR THR TYR ASP GLU ILE LYS LYS VAL VAL SEQRES 21 A 332 LYS ALA ALA ALA GLU GLY LYS LEU LYS GLY VAL LEU GLY SEQRES 22 A 332 TYR THR GLU ASP ALA VAL VAL SER SER ASP PHE LEU GLY SEQRES 23 A 332 ASP SER HIS SER SER ILE PHE ASP ALA SER ALA GLY ILE SEQRES 24 A 332 GLN LEU SER PRO LYS PHE VAL LYS LEU VAL SER TRP TYR SEQRES 25 A 332 ASP ASN GLU TYR GLY TYR SER THR ARG VAL VAL ASP LEU SEQRES 26 A 332 VAL GLU HIS VAL ALA LYS ALA SEQRES 1 B 332 MET VAL ARG VAL ALA ILE ASN GLY PHE GLY ARG ILE GLY SEQRES 2 B 332 ARG LEU VAL MET ARG ILE ALA LEU SER ARG PRO ASN VAL SEQRES 3 B 332 GLU VAL VAL ALA LEU ASN ASP PRO PHE ILE THR ASN ASP SEQRES 4 B 332 TYR ALA ALA TYR MET PHE LYS TYR ASP SER THR HIS GLY SEQRES 5 B 332 ARG TYR ALA GLY GLU VAL SER HIS ASP ASP LYS HIS ILE SEQRES 6 B 332 ILE VAL ASP GLY LYS LYS ILE ALA THR TYR GLN GLU ARG SEQRES 7 B 332 ASP PRO ALA ASN LEU PRO TRP GLY SER SER ASN VAL ASP SEQRES 8 B 332 ILE ALA ILE ASP SER THR GLY VAL PHE LYS GLU LEU ASP SEQRES 9 B 332 THR ALA GLN LYS HIS ILE ASP ALA GLY ALA LYS LYS VAL SEQRES 10 B 332 VAL ILE THR ALA PRO SER SER THR ALA PRO MET PHE VAL SEQRES 11 B 332 MET GLY VAL ASN GLU GLU LYS TYR THR SER ASP LEU LYS SEQRES 12 B 332 ILE VAL SER ASN ALA SER CYS THR THR ASN CYS LEU ALA SEQRES 13 B 332 PRO LEU ALA LYS VAL ILE ASN ASP ALA PHE GLY ILE GLU SEQRES 14 B 332 GLU GLY LEU MET THR THR VAL HIS SER LEU THR ALA THR SEQRES 15 B 332 GLN LYS THR VAL ASP GLY PRO SER HIS LYS ASP TRP ARG SEQRES 16 B 332 GLY GLY ARG THR ALA SER GLY ASN ILE ILE PRO SER SER SEQRES 17 B 332 THR GLY ALA ALA LYS ALA VAL GLY LYS VAL LEU PRO GLU SEQRES 18 B 332 LEU GLN GLY LYS LEU THR GLY MET ALA PHE ARG VAL PRO SEQRES 19 B 332 THR VAL ASP VAL SER VAL VAL ASP LEU THR VAL LYS LEU SEQRES 20 B 332 ASN LYS GLU THR THR TYR ASP GLU ILE LYS LYS VAL VAL SEQRES 21 B 332 LYS ALA ALA ALA GLU GLY LYS LEU LYS GLY VAL LEU GLY SEQRES 22 B 332 TYR THR GLU ASP ALA VAL VAL SER SER ASP PHE LEU GLY SEQRES 23 B 332 ASP SER HIS SER SER ILE PHE ASP ALA SER ALA GLY ILE SEQRES 24 B 332 GLN LEU SER PRO LYS PHE VAL LYS LEU VAL SER TRP TYR SEQRES 25 B 332 ASP ASN GLU TYR GLY TYR SER THR ARG VAL VAL ASP LEU SEQRES 26 B 332 VAL GLU HIS VAL ALA LYS ALA HET NAD A 333 44 HET MRY A 334 8 HET NAD B 333 44 HET MRY B 334 8 HET NA B 504 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM MRY MESO-ERYTHRITOL HETNAM NA SODIUM ION FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 MRY 2(C4 H10 O4) FORMUL 7 NA NA 1+ FORMUL 8 HOH *492(H2 O) HELIX 1 1 GLY A 10 ARG A 23 1 14 HELIX 2 2 THR A 37 TYR A 47 1 11 HELIX 3 3 ASP A 79 LEU A 83 5 5 HELIX 4 4 GLU A 102 ALA A 112 1 11 HELIX 5 5 ASN A 134 TYR A 138 5 5 HELIX 6 6 SER A 149 GLY A 167 1 19 HELIX 7 7 TRP A 194 ARG A 198 5 5 HELIX 8 8 THR A 199 ASN A 203 5 5 HELIX 9 9 GLY A 210 LEU A 219 1 10 HELIX 10 10 PRO A 220 GLN A 223 5 4 HELIX 11 11 THR A 252 GLY A 266 1 15 HELIX 12 12 VAL A 280 LEU A 285 5 6 HELIX 13 13 SER A 296 GLY A 298 5 3 HELIX 14 14 GLU A 315 ALA A 332 1 18 HELIX 15 15 GLY B 10 LEU B 21 1 12 HELIX 16 16 THR B 37 TYR B 47 1 11 HELIX 17 17 ASP B 79 LEU B 83 5 5 HELIX 18 18 TRP B 85 ASN B 89 5 5 HELIX 19 19 GLU B 102 ALA B 112 1 11 HELIX 20 20 ASN B 134 TYR B 138 5 5 HELIX 21 21 SER B 149 GLY B 167 1 19 HELIX 22 22 TRP B 194 ARG B 198 5 5 HELIX 23 23 THR B 199 ASN B 203 5 5 HELIX 24 24 GLY B 210 LEU B 219 1 10 HELIX 25 25 PRO B 220 GLN B 223 5 4 HELIX 26 26 THR B 252 GLY B 266 1 15 HELIX 27 27 VAL B 280 LEU B 285 5 6 HELIX 28 28 SER B 296 GLY B 298 5 3 HELIX 29 29 GLU B 315 ALA B 332 1 18 SHEET 1 A 8 VAL A 58 HIS A 60 0 SHEET 2 A 8 HIS A 64 VAL A 67 -1 O ILE A 66 N SER A 59 SHEET 3 A 8 LYS A 70 TYR A 75 -1 O ILE A 72 N ILE A 65 SHEET 4 A 8 GLU A 27 ASN A 32 1 N LEU A 31 O ALA A 73 SHEET 5 A 8 ARG A 3 ASN A 7 1 N VAL A 4 O VAL A 29 SHEET 6 A 8 ILE A 92 ASP A 95 1 O ILE A 94 N ALA A 5 SHEET 7 A 8 LYS A 116 ILE A 119 1 O VAL A 118 N ASP A 95 SHEET 8 A 8 ILE A 144 SER A 146 1 O VAL A 145 N ILE A 119 SHEET 1 B 7 ILE A 205 SER A 208 0 SHEET 2 B 7 LEU A 226 VAL A 233 -1 O ARG A 232 N ILE A 205 SHEET 3 B 7 ILE A 168 SER A 178 1 N HIS A 177 O PHE A 231 SHEET 4 B 7 SER A 239 LEU A 247 -1 O THR A 244 N LEU A 172 SHEET 5 B 7 PHE A 305 TYR A 312 -1 O SER A 310 N VAL A 241 SHEET 6 B 7 SER A 291 ASP A 294 -1 N ASP A 294 O VAL A 309 SHEET 7 B 7 LEU A 272 THR A 275 1 N GLY A 273 O SER A 291 SHEET 1 C 6 ILE A 205 SER A 208 0 SHEET 2 C 6 LEU A 226 VAL A 233 -1 O ARG A 232 N ILE A 205 SHEET 3 C 6 ILE A 168 SER A 178 1 N HIS A 177 O PHE A 231 SHEET 4 C 6 SER A 239 LEU A 247 -1 O THR A 244 N LEU A 172 SHEET 5 C 6 PHE A 305 TYR A 312 -1 O SER A 310 N VAL A 241 SHEET 6 C 6 ILE A 299 SER A 302 -1 N ILE A 299 O LYS A 307 SHEET 1 D 8 VAL B 58 ASP B 61 0 SHEET 2 D 8 HIS B 64 VAL B 67 -1 O HIS B 64 N ASP B 61 SHEET 3 D 8 LYS B 70 TYR B 75 -1 O ILE B 72 N ILE B 65 SHEET 4 D 8 GLU B 27 ASN B 32 1 N LEU B 31 O TYR B 75 SHEET 5 D 8 ARG B 3 ASN B 7 1 N VAL B 4 O GLU B 27 SHEET 6 D 8 ILE B 92 ASP B 95 1 O ILE B 94 N ALA B 5 SHEET 7 D 8 LYS B 116 ILE B 119 1 O VAL B 118 N ASP B 95 SHEET 8 D 8 ILE B 144 SER B 146 1 O VAL B 145 N ILE B 119 SHEET 1 E 7 ILE B 205 SER B 208 0 SHEET 2 E 7 LEU B 226 VAL B 233 -1 O ALA B 230 N SER B 207 SHEET 3 E 7 ILE B 168 SER B 178 1 N HIS B 177 O PHE B 231 SHEET 4 E 7 SER B 239 LEU B 247 -1 O ASP B 242 N THR B 174 SHEET 5 E 7 PHE B 305 TYR B 312 -1 O SER B 310 N VAL B 241 SHEET 6 E 7 SER B 291 ASP B 294 -1 N ASP B 294 O VAL B 309 SHEET 7 E 7 LEU B 272 THR B 275 1 N GLY B 273 O SER B 291 SHEET 1 F 6 ILE B 205 SER B 208 0 SHEET 2 F 6 LEU B 226 VAL B 233 -1 O ALA B 230 N SER B 207 SHEET 3 F 6 ILE B 168 SER B 178 1 N HIS B 177 O PHE B 231 SHEET 4 F 6 SER B 239 LEU B 247 -1 O ASP B 242 N THR B 174 SHEET 5 F 6 PHE B 305 TYR B 312 -1 O SER B 310 N VAL B 241 SHEET 6 F 6 ILE B 299 SER B 302 -1 N ILE B 299 O LYS B 307 LINK O ALA B 20 NA NA B 504 1555 1555 2.60 LINK O ARG B 23 NA NA B 504 1555 1555 2.52 LINK O VAL B 26 NA NA B 504 1555 1555 2.57 LINK NA NA B 504 O HOH B 519 1555 1555 2.69 CISPEP 1 MET A 1 VAL A 2 0 -4.73 SITE 1 AC1 24 ASN A 7 GLY A 8 GLY A 10 ARG A 11 SITE 2 AC1 24 ILE A 12 ASP A 33 PRO A 34 ARG A 78 SITE 3 AC1 24 SER A 96 THR A 97 GLY A 98 THR A 120 SITE 4 AC1 24 ALA A 121 CYS A 150 ALA A 181 ASN A 314 SITE 5 AC1 24 TYR A 318 HOH A 360 HOH A 377 HOH A 409 SITE 6 AC1 24 HOH A 447 HOH A 566 HOH B 380 HOH B 456 SITE 1 AC2 6 ALA A 42 TYR A 43 VAL A 58 HIS A 60 SITE 2 AC2 6 HOH A 385 ASP B 277 SITE 1 AC3 20 HOH A 397 ASN B 7 GLY B 8 GLY B 10 SITE 2 AC3 20 ARG B 11 ILE B 12 ASP B 33 PRO B 34 SITE 3 AC3 20 SER B 96 THR B 97 GLY B 98 THR B 120 SITE 4 AC3 20 ALA B 121 CYS B 150 ALA B 181 ASN B 314 SITE 5 AC3 20 TYR B 318 HOH B 400 HOH B 411 HOH B 534 SITE 1 AC4 6 ASP A 277 ALA B 42 TYR B 43 VAL B 58 SITE 2 AC4 6 HOH B 379 HOH B 434 SITE 1 AC5 5 ALA B 20 LEU B 21 ARG B 23 VAL B 26 SITE 2 AC5 5 HOH B 519 CRYST1 121.834 131.052 96.685 90.00 90.00 90.00 C 2 2 21 16 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 0.008208 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010343 0.00000