HEADER ISOMERASE 16-OCT-13 4N7T TITLE CRYSTAL STRUCTURE OF PHOSPHORYLATED PHOSPHOPENTOMUTASE FROM TITLE 2 STREPTOCOCCUS MUTANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOPENTOMUTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHODEOXYRIBOMUTASE; COMPND 5 EC: 5.4.2.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS MUTANS; SOURCE 3 ORGANISM_TAXID: 210007; SOURCE 4 STRAIN: ATCC 700610 / UA159; SOURCE 5 GENE: DEOB, SMU_1233; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, NEW YORK SGX KEYWDS 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS, NEW YORK STRUCTURAL KEYWDS 3 GENOMICS RESEARCH CONSORTIUM, NYSGXRC, NYSGRC, PHOSPHORYLATED KEYWDS 4 PHOSPHOPENTOMUTASE, MANGANESE BINDING, PHOSPHORYLATED THR 92 IN THE KEYWDS 5 ACTIVE SITE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,J.BONANNO,S.K.BURLEY,S.C.ALMO,NEW YORK SGX AUTHOR 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC),NEW YORK AUTHOR 3 STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NYSGRC) REVDAT 4 20-SEP-23 4N7T 1 REMARK REVDAT 3 10-FEB-21 4N7T 1 AUTHOR JRNL REMARK SEQADV REVDAT 3 2 1 LINK REVDAT 2 27-NOV-13 4N7T 1 KEYWDS REVDAT 1 06-NOV-13 4N7T 0 JRNL AUTH A.A.FEDOROV,E.V.FEDOROV,J.BONANNO,S.K.BURLEY,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF PHOSPHORYLATED PHOSPHOPENTOMUTASE FROM JRNL TITL 2 STREPTOCOCCUS MUTANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 29.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 61424 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1871 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 29.2712 - 4.6882 0.98 4637 166 0.1544 0.1712 REMARK 3 2 4.6882 - 3.7236 0.99 4613 147 0.1448 0.1668 REMARK 3 3 3.7236 - 3.2536 1.00 4623 166 0.1740 0.1997 REMARK 3 4 3.2536 - 2.9564 1.00 4620 147 0.1837 0.2142 REMARK 3 5 2.9564 - 2.7447 1.00 4597 148 0.1868 0.2356 REMARK 3 6 2.7447 - 2.5830 1.00 4615 142 0.1876 0.2071 REMARK 3 7 2.5830 - 2.4537 1.00 4595 131 0.1845 0.2263 REMARK 3 8 2.4537 - 2.3469 1.00 4595 135 0.1802 0.2551 REMARK 3 9 2.3469 - 2.2566 0.99 4555 123 0.1793 0.2307 REMARK 3 10 2.2566 - 2.1788 0.99 4593 134 0.1785 0.2072 REMARK 3 11 2.1788 - 2.1107 0.99 4584 130 0.1739 0.2172 REMARK 3 12 2.1107 - 2.0504 0.99 4520 138 0.1765 0.2725 REMARK 3 13 2.0504 - 1.9964 0.96 4406 164 0.1934 0.2540 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.820 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) : 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 6359 REMARK 3 ANGLE : 1.040 8646 REMARK 3 CHIRALITY : 0.073 969 REMARK 3 PLANARITY : 0.005 1131 REMARK 3 DIHEDRAL : 11.897 2298 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 13.5245 31.5063 18.9330 REMARK 3 T TENSOR REMARK 3 T11: 0.1660 T22: 0.1788 REMARK 3 T33: 0.1985 T12: 0.0099 REMARK 3 T13: 0.0093 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 1.5529 L22: 0.7529 REMARK 3 L33: 1.4137 L12: -0.0272 REMARK 3 L13: -0.1590 L23: -0.1057 REMARK 3 S TENSOR REMARK 3 S11: 0.0504 S12: -0.0969 S13: 0.3681 REMARK 3 S21: 0.0296 S22: 0.0282 S23: -0.0301 REMARK 3 S31: -0.2521 S32: 0.0557 S33: -0.0520 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 46.0590 15.3004 33.2624 REMARK 3 T TENSOR REMARK 3 T11: 0.1843 T22: 0.1364 REMARK 3 T33: 0.1450 T12: 0.0072 REMARK 3 T13: -0.0279 T23: 0.0548 REMARK 3 L TENSOR REMARK 3 L11: 2.2799 L22: 0.8443 REMARK 3 L33: 1.2528 L12: 0.1212 REMARK 3 L13: -0.5241 L23: -0.3072 REMARK 3 S TENSOR REMARK 3 S11: 0.0053 S12: -0.0537 S13: -0.0106 REMARK 3 S21: 0.1979 S22: -0.0450 S23: -0.0357 REMARK 3 S31: -0.0414 S32: 0.0288 S33: 0.0309 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 4N7T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082860. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61424 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.996 REMARK 200 RESOLUTION RANGE LOW (A) : 29.268 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 3M7V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG 3350, 0.1M BIS-TRIS, 0.2M REMARK 280 LITHIUM SULFATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.0K 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 31.84350 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 MET A -1 REMARK 465 SER A 0 REMARK 465 LEU A 1 REMARK 465 GLU A 404 REMARK 465 GLY A 405 REMARK 465 HIS A 406 REMARK 465 HIS A 407 REMARK 465 HIS A 408 REMARK 465 HIS A 409 REMARK 465 HIS A 410 REMARK 465 HIS A 411 REMARK 465 MET B -1 REMARK 465 SER B 0 REMARK 465 LEU B 1 REMARK 465 SER B 2 REMARK 465 GLU B 404 REMARK 465 GLY B 405 REMARK 465 HIS B 406 REMARK 465 HIS B 407 REMARK 465 HIS B 408 REMARK 465 HIS B 409 REMARK 465 HIS B 410 REMARK 465 HIS B 411 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 SER A 14 6.86 83.11 REMARK 500 ASP A 37 87.84 -173.79 REMARK 500 LEU A 48 110.43 -166.77 REMARK 500 THR A 81 -167.05 -166.76 REMARK 500 ARG A 206 72.32 -119.67 REMARK 500 ASN A 214 71.81 -171.24 REMARK 500 HIS A 340 -170.92 175.48 REMARK 500 ASN A 342 74.11 -163.51 REMARK 500 THR A 349 18.80 -141.71 REMARK 500 ALA A 392 -122.59 -91.26 REMARK 500 SER B 14 7.10 81.73 REMARK 500 ASP B 37 90.31 -172.91 REMARK 500 LEU B 48 111.80 -161.72 REMARK 500 THR B 81 -168.24 -163.92 REMARK 500 ARG B 213 -5.07 67.85 REMARK 500 HIS B 340 -171.50 174.82 REMARK 500 ASN B 342 80.25 -161.45 REMARK 500 THR B 349 18.29 -140.69 REMARK 500 ALA B 392 -117.34 -93.48 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 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 13 OD1 54.3 REMARK 620 3 TPO A 92 OG1 126.7 97.6 REMARK 620 4 TPO A 92 O2P 66.8 69.9 60.8 REMARK 620 5 ASP A 339 OD2 120.0 86.0 98.3 144.1 REMARK 620 6 HIS A 340 NE2 103.9 155.8 105.1 114.2 98.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TPO A 92 O1P REMARK 620 2 ASP A 298 OD1 94.6 REMARK 620 3 HIS A 303 NE2 156.3 101.9 REMARK 620 4 HIS A 351 NE2 88.6 119.6 97.7 REMARK 620 5 HOH A 753 O 64.3 106.1 94.5 128.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 13 OD2 REMARK 620 2 ASP B 13 OD1 53.0 REMARK 620 3 TPO B 92 OG1 127.6 99.8 REMARK 620 4 TPO B 92 O2P 70.4 77.8 59.6 REMARK 620 5 ASP B 339 OD2 117.2 84.3 100.0 149.3 REMARK 620 6 HIS B 340 NE2 106.6 155.2 104.5 110.6 96.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TPO B 92 O1P REMARK 620 2 ASP B 298 OD1 100.6 REMARK 620 3 HIS B 303 NE2 155.8 97.7 REMARK 620 4 HIS B 351 NE2 85.3 115.6 100.9 REMARK 620 5 HOH B 757 O 74.2 156.0 82.6 87.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M7V RELATED DB: PDB REMARK 900 THE SAME ENZYME WITHOUT MODELLING OF PHOSPHORYLATED THREONINE IN REMARK 900 THE ACTIVE SITE REMARK 900 RELATED ID: NYSGXRC-6197F RELATED DB: TARGETTRACK DBREF 4N7T A 2 403 UNP Q8DTU0 DEOB_STRMU 2 403 DBREF 4N7T B 2 403 UNP Q8DTU0 DEOB_STRMU 2 403 SEQADV 4N7T MET A -1 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T SER A 0 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T LEU A 1 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T GLU A 404 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T GLY A 405 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS A 406 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS A 407 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS A 408 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS A 409 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS A 410 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS A 411 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T MET B -1 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T SER B 0 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T LEU B 1 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T GLU B 404 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T GLY B 405 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS B 406 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS B 407 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS B 408 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS B 409 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS B 410 UNP Q8DTU0 EXPRESSION TAG SEQADV 4N7T HIS B 411 UNP Q8DTU0 EXPRESSION TAG SEQRES 1 A 413 MET SER LEU SER THR PHE ASN ARG ILE HIS LEU VAL VAL SEQRES 2 A 413 LEU ASP SER VAL GLY ILE GLY ALA ALA PRO ASP ALA ASN SEQRES 3 A 413 ASN PHE SER ASN ALA GLY VAL PRO ASP GLY ALA SER ASP SEQRES 4 A 413 THR LEU GLY HIS ILE SER LYS THR VAL GLY LEU ASN VAL SEQRES 5 A 413 PRO ASN MET ALA LYS ILE GLY LEU GLY ASN ILE PRO ARG SEQRES 6 A 413 ASP THR PRO LEU LYS THR VAL PRO ALA GLU ASN HIS PRO SEQRES 7 A 413 THR GLY TYR VAL THR LYS LEU GLU GLU VAL SER LEU GLY SEQRES 8 A 413 LYS ASP TPO MET THR GLY HIS TRP GLU ILE MET GLY LEU SEQRES 9 A 413 ASN ILE THR GLU PRO PHE ASP THR PHE TRP ASN GLY PHE SEQRES 10 A 413 PRO GLU GLU ILE ILE SER LYS ILE GLU LYS PHE SER GLY SEQRES 11 A 413 ARG LYS VAL ILE ARG GLU ALA ASN LYS PRO TYR SER GLY SEQRES 12 A 413 THR ALA VAL ILE ASP ASP PHE GLY PRO ARG GLN MET GLU SEQRES 13 A 413 THR GLY GLU LEU ILE ILE TYR THR SER ALA ASP PRO VAL SEQRES 14 A 413 LEU GLN ILE ALA ALA HIS GLU ASP VAL ILE PRO LEU ASP SEQRES 15 A 413 GLU LEU TYR ARG ILE CYS GLU TYR ALA ARG SER ILE THR SEQRES 16 A 413 LEU GLU ARG PRO ALA LEU LEU GLY ARG ILE ILE ALA ARG SEQRES 17 A 413 PRO TYR VAL GLY LYS PRO ARG ASN PHE THR ARG THR ALA SEQRES 18 A 413 ASN ARG HIS ASP TYR ALA LEU SER PRO PHE ALA PRO THR SEQRES 19 A 413 VAL LEU ASN LYS LEU ALA ASP ALA GLY VAL SER THR TYR SEQRES 20 A 413 ALA VAL GLY LYS ILE ASN ASP ILE PHE ASN GLY SER GLY SEQRES 21 A 413 ILE THR ASN ASP MET GLY HIS ASN LYS SER ASN SER HIS SEQRES 22 A 413 GLY VAL ASP THR LEU ILE LYS THR MET GLY LEU SER ALA SEQRES 23 A 413 PHE THR LYS GLY PHE SER PHE THR ASN LEU VAL ASP PHE SEQRES 24 A 413 ASP ALA LEU TYR GLY HIS ARG ARG ASN ALA HIS GLY TYR SEQRES 25 A 413 ARG ASP CYS LEU HIS GLU PHE ASP GLU ARG LEU PRO GLU SEQRES 26 A 413 ILE ILE ALA ALA MET LYS VAL ASP ASP LEU LEU LEU ILE SEQRES 27 A 413 THR ALA ASP HIS GLY ASN ASP PRO THR TYR ALA GLY THR SEQRES 28 A 413 ASP HIS THR ARG GLU TYR VAL PRO LEU LEU ALA TYR SER SEQRES 29 A 413 PRO SER PHE THR GLY ASN GLY VAL LEU PRO VAL GLY HIS SEQRES 30 A 413 TYR ALA ASP ILE SER ALA THR ILE ALA ASP ASN PHE GLY SEQRES 31 A 413 VAL ASP THR ALA MET ILE GLY GLU SER PHE LEU ASP LYS SEQRES 32 A 413 LEU ILE GLU GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 413 MET SER LEU SER THR PHE ASN ARG ILE HIS LEU VAL VAL SEQRES 2 B 413 LEU ASP SER VAL GLY ILE GLY ALA ALA PRO ASP ALA ASN SEQRES 3 B 413 ASN PHE SER ASN ALA GLY VAL PRO ASP GLY ALA SER ASP SEQRES 4 B 413 THR LEU GLY HIS ILE SER LYS THR VAL GLY LEU ASN VAL SEQRES 5 B 413 PRO ASN MET ALA LYS ILE GLY LEU GLY ASN ILE PRO ARG SEQRES 6 B 413 ASP THR PRO LEU LYS THR VAL PRO ALA GLU ASN HIS PRO SEQRES 7 B 413 THR GLY TYR VAL THR LYS LEU GLU GLU VAL SER LEU GLY SEQRES 8 B 413 LYS ASP TPO MET THR GLY HIS TRP GLU ILE MET GLY LEU SEQRES 9 B 413 ASN ILE THR GLU PRO PHE ASP THR PHE TRP ASN GLY PHE SEQRES 10 B 413 PRO GLU GLU ILE ILE SER LYS ILE GLU LYS PHE SER GLY SEQRES 11 B 413 ARG LYS VAL ILE ARG GLU ALA ASN LYS PRO TYR SER GLY SEQRES 12 B 413 THR ALA VAL ILE ASP ASP PHE GLY PRO ARG GLN MET GLU SEQRES 13 B 413 THR GLY GLU LEU ILE ILE TYR THR SER ALA ASP PRO VAL SEQRES 14 B 413 LEU GLN ILE ALA ALA HIS GLU ASP VAL ILE PRO LEU ASP SEQRES 15 B 413 GLU LEU TYR ARG ILE CYS GLU TYR ALA ARG SER ILE THR SEQRES 16 B 413 LEU GLU ARG PRO ALA LEU LEU GLY ARG ILE ILE ALA ARG SEQRES 17 B 413 PRO TYR VAL GLY LYS PRO ARG ASN PHE THR ARG THR ALA SEQRES 18 B 413 ASN ARG HIS ASP TYR ALA LEU SER PRO PHE ALA PRO THR SEQRES 19 B 413 VAL LEU ASN LYS LEU ALA ASP ALA GLY VAL SER THR TYR SEQRES 20 B 413 ALA VAL GLY LYS ILE ASN ASP ILE PHE ASN GLY SER GLY SEQRES 21 B 413 ILE THR ASN ASP MET GLY HIS ASN LYS SER ASN SER HIS SEQRES 22 B 413 GLY VAL ASP THR LEU ILE LYS THR MET GLY LEU SER ALA SEQRES 23 B 413 PHE THR LYS GLY PHE SER PHE THR ASN LEU VAL ASP PHE SEQRES 24 B 413 ASP ALA LEU TYR GLY HIS ARG ARG ASN ALA HIS GLY TYR SEQRES 25 B 413 ARG ASP CYS LEU HIS GLU PHE ASP GLU ARG LEU PRO GLU SEQRES 26 B 413 ILE ILE ALA ALA MET LYS VAL ASP ASP LEU LEU LEU ILE SEQRES 27 B 413 THR ALA ASP HIS GLY ASN ASP PRO THR TYR ALA GLY THR SEQRES 28 B 413 ASP HIS THR ARG GLU TYR VAL PRO LEU LEU ALA TYR SER SEQRES 29 B 413 PRO SER PHE THR GLY ASN GLY VAL LEU PRO VAL GLY HIS SEQRES 30 B 413 TYR ALA ASP ILE SER ALA THR ILE ALA ASP ASN PHE GLY SEQRES 31 B 413 VAL ASP THR ALA MET ILE GLY GLU SER PHE LEU ASP LYS SEQRES 32 B 413 LEU ILE GLU GLY HIS HIS HIS HIS HIS HIS MODRES 4N7T TPO A 92 THR PHOSPHOTHREONINE MODRES 4N7T TPO B 92 THR PHOSPHOTHREONINE HET TPO A 92 11 HET TPO B 92 11 HET MN A 501 1 HET MN A 502 1 HET SO4 A 503 5 HET GOL A 504 6 HET GOL A 505 6 HET AZI A 506 3 HET PEG A 507 7 HET GOL A 508 6 HET MN B 501 1 HET MN B 502 1 HET SO4 B 503 5 HET AZI B 504 3 HETNAM TPO PHOSPHOTHREONINE HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM AZI AZIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN TPO PHOSPHONOTHREONINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 TPO 2(C4 H10 N O6 P) FORMUL 3 MN 4(MN 2+) FORMUL 5 SO4 2(O4 S 2-) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 8 AZI 2(N3 1-) FORMUL 9 PEG C4 H10 O3 FORMUL 15 HOH *361(H2 O) HELIX 1 1 ASP A 22 ASN A 25 5 4 HELIX 2 2 GLY A 34 SER A 36 5 3 HELIX 3 3 ASP A 37 VAL A 46 1 10 HELIX 4 4 VAL A 50 GLY A 57 1 8 HELIX 5 5 LEU A 58 ILE A 61 5 4 HELIX 6 6 ASP A 91 MET A 100 1 10 HELIX 7 7 PRO A 116 GLY A 128 1 13 HELIX 8 8 ILE A 132 ASN A 136 5 5 HELIX 9 9 SER A 140 GLY A 156 1 17 HELIX 10 10 PRO A 178 ILE A 192 1 15 HELIX 11 11 THR A 232 ALA A 240 1 9 HELIX 12 12 LYS A 249 ASN A 255 1 7 HELIX 13 13 SER A 268 LEU A 282 1 15 HELIX 14 14 VAL A 295 LEU A 300 1 6 HELIX 15 15 ASN A 306 ALA A 327 1 22 HELIX 16 16 ALA A 377 GLY A 388 1 12 HELIX 17 17 PHE A 398 ILE A 403 1 6 HELIX 18 18 ASP B 22 ASN B 25 5 4 HELIX 19 19 GLY B 34 SER B 36 5 3 HELIX 20 20 ASP B 37 VAL B 46 1 10 HELIX 21 21 VAL B 50 GLY B 57 1 8 HELIX 22 22 LEU B 58 ILE B 61 5 4 HELIX 23 23 ASP B 91 MET B 100 1 10 HELIX 24 24 PRO B 116 GLY B 128 1 13 HELIX 25 25 ILE B 132 ASN B 136 5 5 HELIX 26 26 SER B 140 GLY B 156 1 17 HELIX 27 27 PRO B 178 ILE B 192 1 15 HELIX 28 28 THR B 232 ALA B 240 1 9 HELIX 29 29 LYS B 249 PHE B 254 1 6 HELIX 30 30 SER B 268 GLY B 281 1 14 HELIX 31 31 VAL B 295 TYR B 301 1 7 HELIX 32 32 ASN B 306 ALA B 327 1 22 HELIX 33 33 ALA B 377 GLY B 388 1 12 HELIX 34 34 PHE B 398 ILE B 403 1 6 SHEET 1 A 8 ASN A 261 ASP A 262 0 SHEET 2 A 8 SER A 243 VAL A 247 1 N ALA A 246 O ASN A 261 SHEET 3 A 8 GLY A 288 LEU A 294 1 O PHE A 289 N TYR A 245 SHEET 4 A 8 ARG A 6 LEU A 12 1 N VAL A 11 O THR A 292 SHEET 5 A 8 ASP A 332 THR A 337 1 O LEU A 335 N VAL A 10 SHEET 6 A 8 VAL A 356 TYR A 361 -1 O TYR A 361 N LEU A 334 SHEET 7 A 8 TYR A 79 GLU A 84 -1 N LEU A 83 O VAL A 356 SHEET 8 A 8 GLY A 369 VAL A 370 1 O GLY A 369 N VAL A 80 SHEET 1 B 8 ASN A 261 ASP A 262 0 SHEET 2 B 8 SER A 243 VAL A 247 1 N ALA A 246 O ASN A 261 SHEET 3 B 8 GLY A 288 LEU A 294 1 O PHE A 289 N TYR A 245 SHEET 4 B 8 ARG A 6 LEU A 12 1 N VAL A 11 O THR A 292 SHEET 5 B 8 ASP A 332 THR A 337 1 O LEU A 335 N VAL A 10 SHEET 6 B 8 VAL A 356 TYR A 361 -1 O TYR A 361 N LEU A 334 SHEET 7 B 8 TYR A 79 GLU A 84 -1 N LEU A 83 O VAL A 356 SHEET 8 B 8 GLY A 374 HIS A 375 1 O GLY A 374 N LYS A 82 SHEET 1 C 2 SER A 27 ASN A 28 0 SHEET 2 C 2 VAL A 31 PRO A 32 -1 O VAL A 31 N ASN A 28 SHEET 1 D 4 ILE A 159 THR A 162 0 SHEET 2 D 4 VAL A 167 HIS A 173 -1 O GLN A 169 N TYR A 161 SHEET 3 D 4 ARG A 202 LYS A 211 1 O ARG A 206 N ILE A 170 SHEET 4 D 4 ASN A 214 ARG A 217 -1 O THR A 216 N VAL A 209 SHEET 1 E 4 ILE A 159 THR A 162 0 SHEET 2 E 4 VAL A 167 HIS A 173 -1 O GLN A 169 N TYR A 161 SHEET 3 E 4 ARG A 202 LYS A 211 1 O ARG A 206 N ILE A 170 SHEET 4 E 4 HIS A 222 ALA A 225 -1 O HIS A 222 N ALA A 205 SHEET 1 F 8 ASN B 261 ASP B 262 0 SHEET 2 F 8 THR B 244 VAL B 247 1 N THR B 244 O ASN B 261 SHEET 3 F 8 GLY B 288 LEU B 294 1 O PHE B 289 N TYR B 245 SHEET 4 F 8 ARG B 6 LEU B 12 1 N VAL B 11 O THR B 292 SHEET 5 F 8 ASP B 332 THR B 337 1 O LEU B 335 N VAL B 10 SHEET 6 F 8 VAL B 356 TYR B 361 -1 O TYR B 361 N LEU B 334 SHEET 7 F 8 TYR B 79 GLU B 84 -1 N LEU B 83 O VAL B 356 SHEET 8 F 8 GLY B 369 VAL B 370 1 O GLY B 369 N VAL B 80 SHEET 1 G 8 ASN B 261 ASP B 262 0 SHEET 2 G 8 THR B 244 VAL B 247 1 N THR B 244 O ASN B 261 SHEET 3 G 8 GLY B 288 LEU B 294 1 O PHE B 289 N TYR B 245 SHEET 4 G 8 ARG B 6 LEU B 12 1 N VAL B 11 O THR B 292 SHEET 5 G 8 ASP B 332 THR B 337 1 O LEU B 335 N VAL B 10 SHEET 6 G 8 VAL B 356 TYR B 361 -1 O TYR B 361 N LEU B 334 SHEET 7 G 8 TYR B 79 GLU B 84 -1 N LEU B 83 O VAL B 356 SHEET 8 G 8 GLY B 374 HIS B 375 1 O GLY B 374 N GLU B 84 SHEET 1 H 2 SER B 27 ASN B 28 0 SHEET 2 H 2 VAL B 31 PRO B 32 -1 O VAL B 31 N ASN B 28 SHEET 1 I 4 ILE B 159 TYR B 161 0 SHEET 2 I 4 VAL B 167 HIS B 173 -1 O GLN B 169 N TYR B 161 SHEET 3 I 4 ARG B 202 LYS B 211 1 O ARG B 206 N ILE B 170 SHEET 4 I 4 ASN B 214 THR B 216 -1 O THR B 216 N VAL B 209 SHEET 1 J 4 ILE B 159 TYR B 161 0 SHEET 2 J 4 VAL B 167 HIS B 173 -1 O GLN B 169 N TYR B 161 SHEET 3 J 4 ARG B 202 LYS B 211 1 O ARG B 206 N ILE B 170 SHEET 4 J 4 HIS B 222 ALA B 225 -1 O HIS B 222 N ALA B 205 LINK C ASP A 91 N TPO A 92 1555 1555 1.33 LINK C TPO A 92 N MET A 93 1555 1555 1.33 LINK C ASP B 91 N TPO B 92 1555 1555 1.33 LINK C TPO B 92 N MET B 93 1555 1555 1.33 LINK OD2 ASP A 13 MN MN A 501 1555 1555 2.02 LINK OD1 ASP A 13 MN MN A 501 1555 1555 2.65 LINK OG1 TPO A 92 MN MN A 501 1555 1555 2.38 LINK O2P TPO A 92 MN MN A 501 1555 1555 2.57 LINK O1P TPO A 92 MN MN A 502 1555 1555 2.36 LINK OD1 ASP A 298 MN MN A 502 1555 1555 2.03 LINK NE2 HIS A 303 MN MN A 502 1555 1555 2.14 LINK OD2 ASP A 339 MN MN A 501 1555 1555 2.07 LINK NE2 HIS A 340 MN MN A 501 1555 1555 2.11 LINK NE2 HIS A 351 MN MN A 502 1555 1555 2.01 LINK MN MN A 502 O HOH A 753 1555 1555 2.19 LINK OD2 ASP B 13 MN MN B 501 1555 1555 1.98 LINK OD1 ASP B 13 MN MN B 501 1555 1555 2.75 LINK OG1 TPO B 92 MN MN B 501 1555 1555 2.45 LINK O2P TPO B 92 MN MN B 501 1555 1555 2.51 LINK O1P TPO B 92 MN MN B 502 1555 1555 2.46 LINK OD1 ASP B 298 MN MN B 502 1555 1555 2.00 LINK NE2 HIS B 303 MN MN B 502 1555 1555 2.10 LINK OD2 ASP B 339 MN MN B 501 1555 1555 2.03 LINK NE2 HIS B 340 MN MN B 501 1555 1555 2.14 LINK NE2 HIS B 351 MN MN B 502 1555 1555 2.08 LINK MN MN B 502 O HOH B 757 1555 1555 2.49 CISPEP 1 ARG A 196 PRO A 197 0 5.06 CISPEP 2 ARG B 196 PRO B 197 0 8.65 SITE 1 AC1 4 ASP A 13 TPO A 92 ASP A 339 HIS A 340 SITE 1 AC2 5 TPO A 92 ASP A 298 HIS A 303 HIS A 351 SITE 2 AC2 5 HOH A 753 SITE 1 AC3 5 GLY A 141 TYR A 161 GLN A 169 ARG A 206 SITE 2 AC3 5 ARG A 217 SITE 1 AC4 5 GLU A 106 PHE A 229 HOH A 776 HOH A 794 SITE 2 AC4 5 HOH B 643 SITE 1 AC5 6 GLY A 59 ASN A 60 ILE A 61 PRO A 62 SITE 2 AC5 6 ARG A 63 PRO A 66 SITE 1 AC6 3 VAL A 273 GLU A 316 ARG A 320 SITE 1 AC7 7 ALA A 35 HIS A 41 LYS A 44 HOH A 687 SITE 2 AC7 7 ALA B 35 LYS B 44 HOH B 622 SITE 1 AC8 8 ALA A 35 HIS A 41 LYS A 44 HOH A 709 SITE 2 AC8 8 HOH A 795 HIS B 41 LYS B 44 HOH B 672 SITE 1 AC9 4 ASP B 13 TPO B 92 ASP B 339 HIS B 340 SITE 1 BC1 5 TPO B 92 ASP B 298 HIS B 303 HIS B 351 SITE 2 BC1 5 HOH B 757 SITE 1 BC2 5 GLY B 141 TYR B 161 GLN B 169 ARG B 206 SITE 2 BC2 5 ARG B 217 SITE 1 BC3 4 VAL B 273 GLU B 316 PHE B 317 ARG B 320 CRYST1 69.788 63.687 104.765 90.00 98.85 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 0.014329 0.000000 0.002232 0.00000 SCALE2 0.000000 0.015702 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009660 0.00000