HEADER HYDROLASE 05-JAN-12 3VDH TITLE CRYSTAL STRUCTURE OF PBGH5A, A GLYCOSIDE HYDROLASE FAMILY 5 ENZYME TITLE 2 FROM PREVOTELLA BRYANTII B14 COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-1,4-ENDOGLUCANASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PREVOTELLA BRYANTII; SOURCE 3 ORGANISM_TAXID: 77095; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET101-11079 KEYWDS ENDO-BETA-GLUCANASE/ENDO-XYLOGLUCANASE, GLYCOSYL HYDROLASE FAMILY 5, KEYWDS 2 MIXED ALPHA-BETA, TIM BARREL, HYDROLASE, STRUCTURAL GENOMICS, PSI- KEYWDS 3 BIOLOGY, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 4 GENOMICS, MCSG EXPDTA X-RAY DIFFRACTION AUTHOR P.J.STOGIOS,E.EVDOKIMOVA,O.EGOROVA,V.YIM,A.JOACHIMIAK,A.M.EDWARDS, AUTHOR 2 A.SAVCHENKO,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 9 06-NOV-24 3VDH 1 REMARK REVDAT 8 06-DEC-23 3VDH 1 REMARK REVDAT 7 13-SEP-23 3VDH 1 REMARK SEQADV LINK REVDAT 6 22-JUN-16 3VDH 1 HEADER KEYWDS TITLE REVDAT 5 17-FEB-16 3VDH 1 JRNL REVDAT 4 23-DEC-15 3VDH 1 JRNL REVDAT 3 04-NOV-15 3VDH 1 JRNL REVDAT 2 16-SEP-15 3VDH 1 REMARK REVDAT 1 18-JAN-12 3VDH 0 SPRSDE 18-JAN-12 3VDH 3L55 JRNL AUTH N.MCGREGOR,M.MORAR,T.H.FENGER,P.STOGIOS,N.LENFANT,V.YIN, JRNL AUTH 2 X.XU,E.EVDOKIMOVA,H.CUI,B.HENRISSAT,A.SAVCHENKO,H.BRUMER JRNL TITL STRUCTURE-FUNCTION ANALYSIS OF A MIXED-LINKAGE JRNL TITL 2 BETA-GLUCANASE/XYLOGLUCANASE FROM THE KEY RUMINAL JRNL TITL 3 BACTEROIDETES PREVOTELLA BRYANTII B14. JRNL REF J.BIOL.CHEM. V. 291 1175 2016 JRNL REFN ISSN 0021-9258 JRNL PMID 26507654 JRNL DOI 10.1074/JBC.M115.691659 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 79400 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) : 0.151 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.460 REMARK 3 FREE R VALUE TEST SET COUNT : 1951 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 26.3571 - 3.4878 0.95 8203 212 0.1387 0.1703 REMARK 3 2 3.4878 - 2.7693 0.95 8056 200 0.1406 0.1868 REMARK 3 3 2.7693 - 2.4195 0.94 8042 193 0.1438 0.1905 REMARK 3 4 2.4195 - 2.1984 0.93 7892 203 0.1364 0.2184 REMARK 3 5 2.1984 - 2.0409 0.92 7781 195 0.1409 0.1792 REMARK 3 6 2.0409 - 1.9206 0.91 7694 191 0.1544 0.2477 REMARK 3 7 1.9206 - 1.8245 0.91 7660 189 0.1653 0.2299 REMARK 3 8 1.8245 - 1.7451 0.90 7565 191 0.1974 0.2465 REMARK 3 9 1.7451 - 1.6779 0.89 7580 195 0.2423 0.2847 REMARK 3 10 1.6779 - 1.6200 0.84 6976 182 0.2939 0.3161 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 : 0.35 REMARK 3 B_SOL : 55.55 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.220 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) : 0.58580 REMARK 3 B22 (A**2) : 3.28260 REMARK 3 B33 (A**2) : -0.68020 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.17600 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 : 0.010 5645 REMARK 3 ANGLE : 1.222 7703 REMARK 3 CHIRALITY : 0.086 829 REMARK 3 PLANARITY : 0.006 1005 REMARK 3 DIHEDRAL : 13.094 1987 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 7:206 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1785 36.9674 9.4175 REMARK 3 T TENSOR REMARK 3 T11: 0.1080 T22: 0.3170 REMARK 3 T33: 0.1080 T12: -0.0850 REMARK 3 T13: 0.0169 T23: 0.0477 REMARK 3 L TENSOR REMARK 3 L11: 1.6981 L22: 0.8412 REMARK 3 L33: 1.4341 L12: 0.0922 REMARK 3 L13: 1.3066 L23: -0.3558 REMARK 3 S TENSOR REMARK 3 S11: -0.1934 S12: 0.5452 S13: 0.2443 REMARK 3 S21: -0.1069 S22: 0.0732 S23: -0.1035 REMARK 3 S31: -0.0800 S32: 0.5838 S33: 0.0688 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 207:294 REMARK 3 ORIGIN FOR THE GROUP (A): -12.6268 26.0661 15.4509 REMARK 3 T TENSOR REMARK 3 T11: 0.0918 T22: 0.1151 REMARK 3 T33: 0.1164 T12: -0.0218 REMARK 3 T13: -0.0100 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 1.8541 L22: 1.7010 REMARK 3 L33: 2.3393 L12: 0.1101 REMARK 3 L13: 1.0960 L23: -0.2165 REMARK 3 S TENSOR REMARK 3 S11: 0.0889 S12: 0.0867 S13: -0.1398 REMARK 3 S21: -0.0341 S22: 0.0917 S23: 0.1081 REMARK 3 S31: 0.1810 S32: -0.0614 S33: -0.1717 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 295:353 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6545 14.8285 11.9902 REMARK 3 T TENSOR REMARK 3 T11: 0.3325 T22: 0.2628 REMARK 3 T33: 0.2944 T12: 0.1085 REMARK 3 T13: -0.1297 T23: -0.1595 REMARK 3 L TENSOR REMARK 3 L11: 1.5547 L22: 1.1774 REMARK 3 L33: 0.6532 L12: -0.3929 REMARK 3 L13: 0.8783 L23: -0.5578 REMARK 3 S TENSOR REMARK 3 S11: 0.4270 S12: 0.6481 S13: -0.6428 REMARK 3 S21: -0.2224 S22: 0.0735 S23: -0.0300 REMARK 3 S31: 0.7193 S32: 0.5269 S33: -0.2949 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND RESID 6:179 REMARK 3 ORIGIN FOR THE GROUP (A): 0.3053 22.9597 49.3311 REMARK 3 T TENSOR REMARK 3 T11: 0.0857 T22: 0.1169 REMARK 3 T33: 0.1139 T12: 0.0098 REMARK 3 T13: 0.0069 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 1.3391 L22: 1.5198 REMARK 3 L33: 1.6181 L12: 0.1357 REMARK 3 L13: 0.7948 L23: 0.0615 REMARK 3 S TENSOR REMARK 3 S11: 0.0585 S12: -0.1319 S13: -0.0128 REMARK 3 S21: 0.0331 S22: -0.0188 S23: 0.1436 REMARK 3 S31: -0.0005 S32: -0.0662 S33: -0.0441 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND RESID 180:294 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0120 31.4178 47.2832 REMARK 3 T TENSOR REMARK 3 T11: 0.1127 T22: 0.1681 REMARK 3 T33: 0.1360 T12: -0.0319 REMARK 3 T13: -0.0225 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 1.5009 L22: 0.8841 REMARK 3 L33: 2.2680 L12: 0.1076 REMARK 3 L13: 0.3259 L23: -0.1408 REMARK 3 S TENSOR REMARK 3 S11: -0.0105 S12: 0.0073 S13: 0.1038 REMARK 3 S21: 0.0363 S22: -0.0792 S23: -0.0705 REMARK 3 S31: -0.3092 S32: 0.3853 S33: 0.0512 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND RESID 295:353 REMARK 3 ORIGIN FOR THE GROUP (A): 17.7423 15.9918 38.7742 REMARK 3 T TENSOR REMARK 3 T11: 0.1327 T22: 0.2911 REMARK 3 T33: 0.1838 T12: 0.0883 REMARK 3 T13: -0.0311 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 1.2769 L22: 1.8454 REMARK 3 L33: 1.3539 L12: 0.0479 REMARK 3 L13: -0.0109 L23: 0.1893 REMARK 3 S TENSOR REMARK 3 S11: 0.1203 S12: 0.1126 S13: -0.1190 REMARK 3 S21: -0.0436 S22: -0.0256 S23: -0.2145 REMARK 3 S31: 0.2232 S32: 0.4869 S33: -0.1113 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 3VDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069907. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83351 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.670 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: PDB ENTRY 2JEQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM ACETATE HYDRATE, 0.1M REMARK 280 SODIUM CACODYLATE PH 6.5, 18% PEG 8K, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K 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 42.62700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 MSE A 1 REMARK 465 ILE A 2 REMARK 465 ASN A 3 REMARK 465 GLN A 4 REMARK 465 ASN A 5 REMARK 465 ALA A 6 REMARK 465 ASN A 353 REMARK 465 MSE B 1 REMARK 465 ILE B 2 REMARK 465 ASN B 3 REMARK 465 GLN B 4 REMARK 465 ASN B 5 REMARK 465 ASN B 353 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MSE A 91 SE 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 NZ LYS A 39 O HOH A 658 2.00 REMARK 500 O HOH A 843 O HOH A 878 2.07 REMARK 500 OD2 ASP B 316 O HOH B 658 2.12 REMARK 500 O HOH A 758 O HOH A 922 2.13 REMARK 500 OE1 GLU A 298 O HOH A 703 2.13 REMARK 500 O HOH A 782 O HOH A 940 2.13 REMARK 500 O HOH B 644 O HOH B 912 2.13 REMARK 500 O HOH A 782 O HOH A 829 2.15 REMARK 500 O HOH A 607 O HOH A 972 2.16 REMARK 500 O HOH B 645 O HOH B 787 2.19 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 THR A 29 -97.81 -120.06 REMARK 500 HIS A 112 -91.31 -103.46 REMARK 500 ALA A 116 -142.73 94.11 REMARK 500 ASP A 152 -169.42 -77.73 REMARK 500 ASN A 161 -81.06 -84.36 REMARK 500 ALA A 211 8.76 59.90 REMARK 500 LYS A 214 29.18 -146.95 REMARK 500 ASP A 288 16.99 57.37 REMARK 500 SER A 319 -165.01 -119.64 REMARK 500 MSE A 325 -52.84 72.07 REMARK 500 PHE A 328 80.94 -151.22 REMARK 500 THR B 29 -98.11 -122.31 REMARK 500 HIS B 112 -88.92 -104.97 REMARK 500 ALA B 116 -146.40 91.73 REMARK 500 ASP B 152 -167.13 -79.79 REMARK 500 ASN B 161 -78.72 -88.00 REMARK 500 LYS B 214 25.58 -148.64 REMARK 500 ASP B 288 18.38 59.60 REMARK 500 SER B 319 -163.15 -113.97 REMARK 500 MSE B 325 -51.16 72.56 REMARK 500 PHE B 328 83.27 -151.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MCSG-APC40456 RELATED DB: TARGETTRACK REMARK 900 RELATED ID: 5D9M RELATED DB: PDB REMARK 900 RELATED ID: 5D9N RELATED DB: PDB REMARK 900 RELATED ID: 5D9O RELATED DB: PDB REMARK 900 RELATED ID: 5D9P RELATED DB: PDB DBREF 3VDH A 2 353 UNP O06842 O06842_PREBR 573 924 DBREF 3VDH B 2 353 UNP O06842 O06842_PREBR 573 924 SEQADV 3VDH MSE A 1 UNP O06842 EXPRESSION TAG SEQADV 3VDH MSE B 1 UNP O06842 EXPRESSION TAG SEQRES 1 A 353 MSE ILE ASN GLN ASN ALA THR TYR MSE GLU GLU SER ALA SEQRES 2 A 353 GLN SER ALA VAL ASP ASN PHE GLY LEU GLY PHE ASN LEU SEQRES 3 A 353 GLY ASN THR LEU ASP ALA ASN GLY CYS GLY THR GLY LYS SEQRES 4 A 353 PRO VAL ALA THR TYR GLU THR PHE TRP GLY GLN PRO GLU SEQRES 5 A 353 THR THR GLN ASP MSE MSE THR PHE LEU MSE GLN ASN GLY SEQRES 6 A 353 PHE ASN ALA VAL ARG ILE PRO VAL THR TRP TYR GLU HIS SEQRES 7 A 353 MSE ASP ALA GLU GLY ASN VAL ASP GLU ALA TRP MSE MSE SEQRES 8 A 353 ARG VAL LYS ALA ILE VAL GLU TYR ALA MSE ASN ALA GLY SEQRES 9 A 353 LEU TYR ALA ILE VAL ASN VAL HIS HIS ASP THR ALA ALA SEQRES 10 A 353 GLY SER GLY ALA TRP ILE LYS ALA ASP THR ASP VAL TYR SEQRES 11 A 353 ALA ALA THR LYS GLU LYS PHE LYS LYS LEU TRP THR GLN SEQRES 12 A 353 ILE ALA ASN ALA LEU ALA ASP TYR ASP GLN HIS LEU LEU SEQRES 13 A 353 PHE GLU GLY TYR ASN GLU MSE LEU ASP GLY ASN ASN SER SEQRES 14 A 353 TRP ASP GLU PRO GLN LYS ALA SER GLY TYR GLU ALA LEU SEQRES 15 A 353 ASN ASN TYR ALA GLN ASP PHE VAL ASP ALA VAL ARG ALA SEQRES 16 A 353 THR GLY GLY ASN ASN ALA THR ARG ASN LEU ILE VAL ASN SEQRES 17 A 353 THR TYR ALA ALA ALA LYS GLY GLU ASN VAL LEU ASN ASN SEQRES 18 A 353 PHE MSE LEU PRO THR ASP ALA VAL ASN ASN HIS LEU ILE SEQRES 19 A 353 VAL GLN VAL HIS SER TYR ASP PRO TRP ASN PHE PHE ASN SEQRES 20 A 353 THR LYS THR THR TRP ASP SER GLU CYS HIS ASN THR LEU SEQRES 21 A 353 THR GLU ILE PHE SER ALA LEU SER LYS LYS PHE THR THR SEQRES 22 A 353 ILE PRO TYR ILE ILE GLY GLU TYR GLY THR HIS GLY GLU SEQRES 23 A 353 SER ASP ILE SER VAL SER LYS SER SER PRO ALA GLU LYS SEQRES 24 A 353 ILE LYS LEU ALA ALA ASP GLN ALA ALA ASP MSE VAL LYS SEQRES 25 A 353 LEU ALA LYS ASP HIS HIS SER ALA THR PHE TYR TRP MSE SEQRES 26 A 353 SER ILE PHE ASP GLY SER ASP ARG ILE GLN PRO GLN TRP SEQRES 27 A 353 SER LEU PRO THR VAL VAL GLU ALA MSE GLN GLU ALA TYR SEQRES 28 A 353 ASN ASN SEQRES 1 B 353 MSE ILE ASN GLN ASN ALA THR TYR MSE GLU GLU SER ALA SEQRES 2 B 353 GLN SER ALA VAL ASP ASN PHE GLY LEU GLY PHE ASN LEU SEQRES 3 B 353 GLY ASN THR LEU ASP ALA ASN GLY CYS GLY THR GLY LYS SEQRES 4 B 353 PRO VAL ALA THR TYR GLU THR PHE TRP GLY GLN PRO GLU SEQRES 5 B 353 THR THR GLN ASP MSE MSE THR PHE LEU MSE GLN ASN GLY SEQRES 6 B 353 PHE ASN ALA VAL ARG ILE PRO VAL THR TRP TYR GLU HIS SEQRES 7 B 353 MSE ASP ALA GLU GLY ASN VAL ASP GLU ALA TRP MSE MSE SEQRES 8 B 353 ARG VAL LYS ALA ILE VAL GLU TYR ALA MSE ASN ALA GLY SEQRES 9 B 353 LEU TYR ALA ILE VAL ASN VAL HIS HIS ASP THR ALA ALA SEQRES 10 B 353 GLY SER GLY ALA TRP ILE LYS ALA ASP THR ASP VAL TYR SEQRES 11 B 353 ALA ALA THR LYS GLU LYS PHE LYS LYS LEU TRP THR GLN SEQRES 12 B 353 ILE ALA ASN ALA LEU ALA ASP TYR ASP GLN HIS LEU LEU SEQRES 13 B 353 PHE GLU GLY TYR ASN GLU MSE LEU ASP GLY ASN ASN SER SEQRES 14 B 353 TRP ASP GLU PRO GLN LYS ALA SER GLY TYR GLU ALA LEU SEQRES 15 B 353 ASN ASN TYR ALA GLN ASP PHE VAL ASP ALA VAL ARG ALA SEQRES 16 B 353 THR GLY GLY ASN ASN ALA THR ARG ASN LEU ILE VAL ASN SEQRES 17 B 353 THR TYR ALA ALA ALA LYS GLY GLU ASN VAL LEU ASN ASN SEQRES 18 B 353 PHE MSE LEU PRO THR ASP ALA VAL ASN ASN HIS LEU ILE SEQRES 19 B 353 VAL GLN VAL HIS SER TYR ASP PRO TRP ASN PHE PHE ASN SEQRES 20 B 353 THR LYS THR THR TRP ASP SER GLU CYS HIS ASN THR LEU SEQRES 21 B 353 THR GLU ILE PHE SER ALA LEU SER LYS LYS PHE THR THR SEQRES 22 B 353 ILE PRO TYR ILE ILE GLY GLU TYR GLY THR HIS GLY GLU SEQRES 23 B 353 SER ASP ILE SER VAL SER LYS SER SER PRO ALA GLU LYS SEQRES 24 B 353 ILE LYS LEU ALA ALA ASP GLN ALA ALA ASP MSE VAL LYS SEQRES 25 B 353 LEU ALA LYS ASP HIS HIS SER ALA THR PHE TYR TRP MSE SEQRES 26 B 353 SER ILE PHE ASP GLY SER ASP ARG ILE GLN PRO GLN TRP SEQRES 27 B 353 SER LEU PRO THR VAL VAL GLU ALA MSE GLN GLU ALA TYR SEQRES 28 B 353 ASN ASN MODRES 3VDH MSE A 9 MET SELENOMETHIONINE MODRES 3VDH MSE A 57 MET SELENOMETHIONINE MODRES 3VDH MSE A 58 MET SELENOMETHIONINE MODRES 3VDH MSE A 62 MET SELENOMETHIONINE MODRES 3VDH MSE A 79 MET SELENOMETHIONINE MODRES 3VDH MSE A 90 MET SELENOMETHIONINE MODRES 3VDH MSE A 91 MET SELENOMETHIONINE MODRES 3VDH MSE A 101 MET SELENOMETHIONINE MODRES 3VDH MSE A 163 MET SELENOMETHIONINE MODRES 3VDH MSE A 223 MET SELENOMETHIONINE MODRES 3VDH MSE A 310 MET SELENOMETHIONINE MODRES 3VDH MSE A 325 MET SELENOMETHIONINE MODRES 3VDH MSE A 347 MET SELENOMETHIONINE MODRES 3VDH MSE B 9 MET SELENOMETHIONINE MODRES 3VDH MSE B 57 MET SELENOMETHIONINE MODRES 3VDH MSE B 58 MET SELENOMETHIONINE MODRES 3VDH MSE B 62 MET SELENOMETHIONINE MODRES 3VDH MSE B 79 MET SELENOMETHIONINE MODRES 3VDH MSE B 90 MET SELENOMETHIONINE MODRES 3VDH MSE B 91 MET SELENOMETHIONINE MODRES 3VDH MSE B 101 MET SELENOMETHIONINE MODRES 3VDH MSE B 163 MET SELENOMETHIONINE MODRES 3VDH MSE B 223 MET SELENOMETHIONINE MODRES 3VDH MSE B 310 MET SELENOMETHIONINE MODRES 3VDH MSE B 325 MET SELENOMETHIONINE MODRES 3VDH MSE B 347 MET SELENOMETHIONINE HET MSE A 9 8 HET MSE A 57 8 HET MSE A 58 8 HET MSE A 62 8 HET MSE A 79 8 HET MSE A 90 8 HET MSE A 91 13 HET MSE A 101 8 HET MSE A 163 8 HET MSE A 223 13 HET MSE A 310 8 HET MSE A 325 8 HET MSE A 347 8 HET MSE B 9 13 HET MSE B 57 8 HET MSE B 58 8 HET MSE B 62 8 HET MSE B 79 8 HET MSE B 90 8 HET MSE B 91 13 HET MSE B 101 8 HET MSE B 163 8 HET MSE B 223 13 HET MSE B 310 8 HET MSE B 325 8 HET MSE B 347 8 HET CL A 401 1 HET CL A 402 1 HET CL B 401 1 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION FORMUL 1 MSE 26(C5 H11 N O2 SE) FORMUL 3 CL 3(CL 1-) FORMUL 6 HOH *912(H2 O) HELIX 1 1 SER A 12 GLY A 21 1 10 HELIX 2 2 PRO A 40 THR A 46 1 7 HELIX 3 3 THR A 54 ASN A 64 1 11 HELIX 4 4 TRP A 75 MSE A 79 5 5 HELIX 5 5 ASP A 86 GLY A 104 1 19 HELIX 6 6 ASP A 126 LEU A 148 1 23 HELIX 7 7 SER A 177 THR A 196 1 20 HELIX 8 8 GLY A 197 THR A 202 5 6 HELIX 9 9 TYR A 210 ALA A 213 5 4 HELIX 10 10 GLY A 215 ASN A 221 1 7 HELIX 11 11 ASN A 244 LYS A 249 1 6 HELIX 12 12 ASP A 253 PHE A 271 1 19 HELIX 13 13 GLY A 285 ILE A 289 5 5 HELIX 14 14 PRO A 296 HIS A 317 1 22 HELIX 15 15 ASP A 329 GLN A 335 5 7 HELIX 16 16 LEU A 340 ASN A 352 1 13 HELIX 17 17 SER B 12 GLY B 21 1 10 HELIX 18 18 PRO B 40 THR B 46 1 7 HELIX 19 19 THR B 54 ASN B 64 1 11 HELIX 20 20 TRP B 75 MSE B 79 5 5 HELIX 21 21 ASP B 86 GLY B 104 1 19 HELIX 22 22 ASP B 126 LEU B 148 1 23 HELIX 23 23 ALA B 176 THR B 196 1 21 HELIX 24 24 GLY B 197 THR B 202 5 6 HELIX 25 25 TYR B 210 ALA B 213 5 4 HELIX 26 26 GLY B 215 ASN B 221 1 7 HELIX 27 27 ASN B 244 LYS B 249 1 6 HELIX 28 28 ASP B 253 PHE B 271 1 19 HELIX 29 29 GLY B 285 ILE B 289 5 5 HELIX 30 30 PRO B 296 HIS B 317 1 22 HELIX 31 31 ASP B 329 GLN B 335 5 7 HELIX 32 32 LEU B 340 ASN B 352 1 13 SHEET 1 A 9 LEU A 22 ASN A 25 0 SHEET 2 A 9 PHE A 66 ILE A 71 1 O ARG A 70 N PHE A 24 SHEET 3 A 9 TYR A 106 ASN A 110 1 O ILE A 108 N ILE A 71 SHEET 4 A 9 LEU A 155 GLU A 158 1 O LEU A 156 N ALA A 107 SHEET 5 A 9 LEU A 205 ASN A 208 1 O ILE A 206 N PHE A 157 SHEET 6 A 9 LEU A 233 SER A 239 1 O ILE A 234 N VAL A 207 SHEET 7 A 9 TYR A 276 TYR A 281 1 O GLU A 280 N SER A 239 SHEET 8 A 9 THR A 321 TRP A 324 1 O TRP A 324 N TYR A 281 SHEET 9 A 9 LEU A 22 ASN A 25 1 N ASN A 25 O TYR A 323 SHEET 1 B 9 LEU B 22 ASN B 25 0 SHEET 2 B 9 PHE B 66 ILE B 71 1 O ARG B 70 N PHE B 24 SHEET 3 B 9 TYR B 106 ASN B 110 1 O ILE B 108 N ILE B 71 SHEET 4 B 9 LEU B 155 GLU B 158 1 O LEU B 156 N ALA B 107 SHEET 5 B 9 LEU B 205 ASN B 208 1 O ILE B 206 N PHE B 157 SHEET 6 B 9 LEU B 233 SER B 239 1 O ILE B 234 N VAL B 207 SHEET 7 B 9 TYR B 276 TYR B 281 1 O GLU B 280 N SER B 239 SHEET 8 B 9 THR B 321 TRP B 324 1 O TRP B 324 N TYR B 281 SHEET 9 B 9 LEU B 22 ASN B 25 1 N ASN B 25 O TYR B 323 LINK C TYR A 8 N MSE A 9 1555 1555 1.32 LINK C MSE A 9 N GLU A 10 1555 1555 1.33 LINK C ASP A 56 N MSE A 57 1555 1555 1.32 LINK C MSE A 57 N MSE A 58 1555 1555 1.33 LINK C MSE A 58 N THR A 59 1555 1555 1.33 LINK C LEU A 61 N MSE A 62 1555 1555 1.33 LINK C MSE A 62 N GLN A 63 1555 1555 1.33 LINK C HIS A 78 N MSE A 79 1555 1555 1.33 LINK C MSE A 79 N ASP A 80 1555 1555 1.33 LINK C TRP A 89 N MSE A 90 1555 1555 1.33 LINK C MSE A 90 N MSE A 91 1555 1555 1.33 LINK C MSE A 91 N ARG A 92 1555 1555 1.34 LINK C ALA A 100 N MSE A 101 1555 1555 1.33 LINK C MSE A 101 N ASN A 102 1555 1555 1.33 LINK C GLU A 162 N MSE A 163 1555 1555 1.33 LINK C MSE A 163 N LEU A 164 1555 1555 1.34 LINK C PHE A 222 N MSE A 223 1555 1555 1.33 LINK C MSE A 223 N LEU A 224 1555 1555 1.33 LINK C ASP A 309 N MSE A 310 1555 1555 1.33 LINK C MSE A 310 N VAL A 311 1555 1555 1.33 LINK C TRP A 324 N MSE A 325 1555 1555 1.34 LINK C MSE A 325 N SER A 326 1555 1555 1.33 LINK C ALA A 346 N MSE A 347 1555 1555 1.33 LINK C MSE A 347 N GLN A 348 1555 1555 1.33 LINK C TYR B 8 N MSE B 9 1555 1555 1.33 LINK C MSE B 9 N GLU B 10 1555 1555 1.33 LINK C ASP B 56 N MSE B 57 1555 1555 1.34 LINK C MSE B 57 N MSE B 58 1555 1555 1.33 LINK C MSE B 58 N THR B 59 1555 1555 1.34 LINK C LEU B 61 N MSE B 62 1555 1555 1.33 LINK C MSE B 62 N GLN B 63 1555 1555 1.33 LINK C HIS B 78 N MSE B 79 1555 1555 1.33 LINK C MSE B 79 N ASP B 80 1555 1555 1.33 LINK C TRP B 89 N MSE B 90 1555 1555 1.33 LINK C MSE B 90 N MSE B 91 1555 1555 1.33 LINK C MSE B 91 N ARG B 92 1555 1555 1.32 LINK C ALA B 100 N MSE B 101 1555 1555 1.34 LINK C MSE B 101 N ASN B 102 1555 1555 1.33 LINK C GLU B 162 N MSE B 163 1555 1555 1.33 LINK C MSE B 163 N LEU B 164 1555 1555 1.34 LINK C PHE B 222 N MSE B 223 1555 1555 1.32 LINK C MSE B 223 N LEU B 224 1555 1555 1.33 LINK C ASP B 309 N MSE B 310 1555 1555 1.33 LINK C MSE B 310 N VAL B 311 1555 1555 1.33 LINK C TRP B 324 N MSE B 325 1555 1555 1.34 LINK C MSE B 325 N SER B 326 1555 1555 1.32 LINK C ALA B 346 N MSE B 347 1555 1555 1.33 LINK C MSE B 347 N GLN B 348 1555 1555 1.33 CISPEP 1 ASP A 241 PRO A 242 0 -6.35 CISPEP 2 GLN A 335 PRO A 336 0 -1.83 CISPEP 3 ASP B 241 PRO B 242 0 -10.95 CISPEP 4 GLN B 335 PRO B 336 0 -8.57 SITE 1 AC1 7 HOH A 954 HOH A 955 HOH A 959 HOH A 960 SITE 2 AC1 7 HOH A 962 HOH A 975 HOH A 976 SITE 1 AC2 7 SER A 119 HOH A 830 HOH A 831 HOH A 832 SITE 2 AC2 7 HOH A 873 HOH B 807 HOH B 812 SITE 1 AC3 6 HOH B 916 HOH B 917 HOH B 918 HOH B 919 SITE 2 AC3 6 HOH B 920 HOH B 921 CRYST1 57.908 85.254 74.556 90.00 109.15 90.00 P 1 21 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 0.017269 0.000000 0.005996 0.00000 SCALE2 0.000000 0.011730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014198 0.00000