HEADER OXIDOREDUCTASE 01-OCT-12 4HCX TITLE STRUCTURE OF ICDH-1 FROM M.TUBERCULOSIS COMPLEXED WITH NADPH & MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP]; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IDH, IDP, NADP(+)-SPECIFIC ICDH, OXALOSUCCINATE COMPND 5 DECARBOXYLASE; COMPND 6 EC: 1.1.1.42; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: ICD, RV3339C, MT3442, MTV016.39C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ICDH-1, ROSSMANN FOLD, DEHYDROGENASE, NADP BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.HAZRA,J.BLANCHARD REVDAT 5 28-FEB-24 4HCX 1 REMARK LINK REVDAT 4 18-APR-18 4HCX 1 REMARK REVDAT 3 18-DEC-13 4HCX 1 JRNL REVDAT 2 04-DEC-13 4HCX 1 FORMUL HET HETATM HETNAM REVDAT 2 2 1 HETSYN REMARK SITE REVDAT 1 27-FEB-13 4HCX 0 JRNL AUTH C.E.QUARTARARO,S.HAZRA,T.HADI,J.S.BLANCHARD JRNL TITL STRUCTURAL, KINETIC AND CHEMICAL MECHANISM OF ISOCITRATE JRNL TITL 2 DEHYDROGENASE-1 FROM MYCOBACTERIUM TUBERCULOSIS. JRNL REF BIOCHEMISTRY V. 52 1765 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23409873 JRNL DOI 10.1021/BI400037W REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 42831 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2279 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL 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) : 34.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.22000 REMARK 3 B22 (A**2) : -1.29000 REMARK 3 B33 (A**2) : 0.07000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4HCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075308. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CU REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42831 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 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 (%) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG2K, 0.1M TRIS HCL PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 45.06750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.44700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.35200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.44700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.06750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.35200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 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 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 2 REMARK 465 ASN A 3 REMARK 465 ALA A 4 REMARK 465 LEU A 407 REMARK 465 ALA A 408 REMARK 465 ASN A 409 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASN B 3 REMARK 465 ALA B 4 REMARK 465 LEU B 407 REMARK 465 ALA B 408 REMARK 465 ASN B 409 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 83 CG CD OE1 OE2 REMARK 470 GLU A 87 CG CD OE1 OE2 REMARK 470 ARG A 232 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 355 CG1 CG2 REMARK 470 LYS A 361 CG CD CE NZ REMARK 470 LYS A 374 CG CD CE NZ REMARK 470 GLU A 386 CG CD OE1 OE2 REMARK 470 ARG B 41 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 87 CG CD OE1 OE2 REMARK 470 LYS B 207 CG CD CE NZ REMARK 470 ARG B 232 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 321 CG CD OE1 NE2 REMARK 470 LYS B 361 CG CD CE NZ 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 NH2 ARG A 103 O HOH A 763 1.21 REMARK 500 OD2 ASP A 388 O HOH A 674 1.85 REMARK 500 ND2 ASN B 331 OD2 ASP B 378 2.00 REMARK 500 O1A NDP B 502 O HOH B 686 2.01 REMARK 500 O HOH A 749 O HOH A 750 2.07 REMARK 500 N ASP B 178 O HOH B 725 2.09 REMARK 500 N SER B 118 O HOH B 721 2.12 REMARK 500 OG SER B 290 OD1 ASP B 378 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 OD2 ASP B 401 O HOH A 674 2455 1.93 REMARK 500 OD1 ASP A 56 NH2 ARG B 143 2444 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS B 76 CB CYS B 76 SG -0.099 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 143 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 197 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 VAL A 297 C - N - CA ANGL. DEV. = 15.6 DEGREES REMARK 500 GLY A 303 N - CA - C ANGL. DEV. = -15.1 DEGREES REMARK 500 PRO A 385 C - N - CD ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG B 143 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 VAL B 297 C - N - CA ANGL. DEV. = 16.5 DEGREES 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 GLU A 20 -142.18 51.18 REMARK 500 THR A 128 -25.48 -162.05 REMARK 500 ASP A 140 -135.24 48.98 REMARK 500 ASP A 150 53.93 -113.55 REMARK 500 GLN A 151 158.91 174.97 REMARK 500 GLU A 177 -55.25 -29.17 REMARK 500 ALA A 244 -52.76 95.94 REMARK 500 ALA A 245 14.36 -148.65 REMARK 500 VAL A 297 62.62 97.26 REMARK 500 SER A 372 -32.91 172.10 REMARK 500 LYS A 405 1.00 -45.04 REMARK 500 LYS B 6 135.25 -34.45 REMARK 500 SER B 10 -81.49 -78.88 REMARK 500 GLU B 20 -135.13 46.61 REMARK 500 ILE B 34 -54.60 -120.18 REMARK 500 ASP B 140 -141.59 46.64 REMARK 500 ASP B 163 -46.07 -22.26 REMARK 500 ARG B 232 -73.56 -54.01 REMARK 500 GLU B 237 -15.98 -144.82 REMARK 500 VAL B 297 67.75 88.43 REMARK 500 SER B 329 70.20 -116.22 REMARK 500 LYS B 374 92.49 82.54 REMARK 500 ASP B 378 -83.99 -5.12 REMARK 500 PRO B 385 -2.41 -49.04 REMARK 500 GLU B 386 116.53 -164.49 REMARK 500 GLN B 387 2.27 -160.12 REMARK 500 ASP B 388 126.18 45.99 REMARK 500 LYS B 405 -2.25 -43.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 243 ALA A 244 44.79 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 B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 255 OD2 REMARK 620 2 HOH A 607 O 73.0 REMARK 620 3 ASP B 278 OD1 91.5 102.0 REMARK 620 4 ASP B 278 O 100.3 171.1 83.6 REMARK 620 5 ASP B 282 OD2 82.5 93.4 161.1 79.8 REMARK 620 6 HOH B 720 O 165.0 100.3 76.6 87.6 111.6 REMARK 620 N 1 2 3 4 5 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 278 OD1 REMARK 620 2 ASP A 278 O 87.6 REMARK 620 3 ASP A 282 OD2 167.5 84.6 REMARK 620 4 HOH A 708 O 82.5 92.0 107.5 REMARK 620 5 ASP B 255 OD2 86.8 99.4 84.8 164.1 REMARK 620 6 HOH B 604 O 97.3 174.5 91.0 86.2 83.5 REMARK 620 N 1 2 3 4 5 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 NDP A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 503 DBREF 4HCX A 1 409 UNP P65097 IDH_MYCTU 1 409 DBREF 4HCX B 1 409 UNP P65097 IDH_MYCTU 1 409 SEQRES 1 A 409 MET SER ASN ALA PRO LYS ILE LYS VAL SER GLY PRO VAL SEQRES 2 A 409 VAL GLU LEU ASP GLY ASP GLU MET THR ARG VAL ILE TRP SEQRES 3 A 409 LYS LEU ILE LYS ASP MET LEU ILE LEU PRO TYR LEU ASP SEQRES 4 A 409 ILE ARG LEU ASP TYR TYR ASP LEU GLY ILE GLU HIS ARG SEQRES 5 A 409 ASP ALA THR ASP ASP GLN VAL THR ILE ASP ALA ALA TYR SEQRES 6 A 409 ALA ILE LYS LYS HIS GLY VAL GLY VAL LYS CYS ALA THR SEQRES 7 A 409 ILE THR PRO ASP GLU ALA ARG VAL GLU GLU PHE ASN LEU SEQRES 8 A 409 LYS LYS MET TRP LEU SER PRO ASN GLY THR ILE ARG ASN SEQRES 9 A 409 ILE LEU GLY GLY THR ILE PHE ARG GLU PRO ILE VAL ILE SEQRES 10 A 409 SER ASN VAL PRO ARG LEU VAL PRO GLY TRP THR LYS PRO SEQRES 11 A 409 ILE VAL ILE GLY ARG HIS ALA PHE GLY ASP GLN TYR ARG SEQRES 12 A 409 ALA THR ASN PHE LYS VAL ASP GLN PRO GLY THR VAL THR SEQRES 13 A 409 LEU THR PHE THR PRO ALA ASP GLY SER ALA PRO ILE VAL SEQRES 14 A 409 HIS GLU MET VAL SER ILE PRO GLU ASP GLY GLY VAL VAL SEQRES 15 A 409 LEU GLY MET TYR ASN PHE LYS GLU SER ILE ARG ASP PHE SEQRES 16 A 409 ALA ARG ALA SER PHE SER TYR GLY LEU ASN ALA LYS TRP SEQRES 17 A 409 PRO VAL TYR LEU SER THR LYS ASN THR ILE LEU LYS ALA SEQRES 18 A 409 TYR ASP GLY MET PHE LYS ASP GLU PHE GLU ARG VAL TYR SEQRES 19 A 409 GLU GLU GLU PHE LYS ALA GLN PHE GLU ALA ALA GLY LEU SEQRES 20 A 409 THR TYR GLU HIS ARG LEU ILE ASP ASP MET VAL ALA ALA SEQRES 21 A 409 CYS LEU LYS TRP GLU GLY GLY TYR VAL TRP ALA CYS LYS SEQRES 22 A 409 ASN TYR ASP GLY ASP VAL GLN SER ASP THR VAL ALA GLN SEQRES 23 A 409 GLY TYR GLY SER LEU GLY LEU MET THR SER VAL LEU MET SEQRES 24 A 409 THR ALA ASP GLY LYS THR VAL GLU ALA GLU ALA ALA HIS SEQRES 25 A 409 GLY THR VAL THR ARG HIS TYR ARG GLN TYR GLN ALA GLY SEQRES 26 A 409 LYS PRO THR SER THR ASN PRO ILE ALA SER ILE PHE ALA SEQRES 27 A 409 TRP THR ARG GLY LEU GLN HIS ARG GLY LYS LEU ASP GLY SEQRES 28 A 409 THR PRO GLU VAL ILE ASP PHE ALA HIS LYS LEU GLU SER SEQRES 29 A 409 VAL VAL ILE ALA THR VAL GLU SER GLY LYS MET THR LYS SEQRES 30 A 409 ASP LEU ALA ILE LEU ILE GLY PRO GLU GLN ASP TRP LEU SEQRES 31 A 409 ASN SER GLU GLU PHE LEU ASP ALA ILE ALA ASP ASN LEU SEQRES 32 A 409 GLU LYS GLU LEU ALA ASN SEQRES 1 B 409 MET SER ASN ALA PRO LYS ILE LYS VAL SER GLY PRO VAL SEQRES 2 B 409 VAL GLU LEU ASP GLY ASP GLU MET THR ARG VAL ILE TRP SEQRES 3 B 409 LYS LEU ILE LYS ASP MET LEU ILE LEU PRO TYR LEU ASP SEQRES 4 B 409 ILE ARG LEU ASP TYR TYR ASP LEU GLY ILE GLU HIS ARG SEQRES 5 B 409 ASP ALA THR ASP ASP GLN VAL THR ILE ASP ALA ALA TYR SEQRES 6 B 409 ALA ILE LYS LYS HIS GLY VAL GLY VAL LYS CYS ALA THR SEQRES 7 B 409 ILE THR PRO ASP GLU ALA ARG VAL GLU GLU PHE ASN LEU SEQRES 8 B 409 LYS LYS MET TRP LEU SER PRO ASN GLY THR ILE ARG ASN SEQRES 9 B 409 ILE LEU GLY GLY THR ILE PHE ARG GLU PRO ILE VAL ILE SEQRES 10 B 409 SER ASN VAL PRO ARG LEU VAL PRO GLY TRP THR LYS PRO SEQRES 11 B 409 ILE VAL ILE GLY ARG HIS ALA PHE GLY ASP GLN TYR ARG SEQRES 12 B 409 ALA THR ASN PHE LYS VAL ASP GLN PRO GLY THR VAL THR SEQRES 13 B 409 LEU THR PHE THR PRO ALA ASP GLY SER ALA PRO ILE VAL SEQRES 14 B 409 HIS GLU MET VAL SER ILE PRO GLU ASP GLY GLY VAL VAL SEQRES 15 B 409 LEU GLY MET TYR ASN PHE LYS GLU SER ILE ARG ASP PHE SEQRES 16 B 409 ALA ARG ALA SER PHE SER TYR GLY LEU ASN ALA LYS TRP SEQRES 17 B 409 PRO VAL TYR LEU SER THR LYS ASN THR ILE LEU LYS ALA SEQRES 18 B 409 TYR ASP GLY MET PHE LYS ASP GLU PHE GLU ARG VAL TYR SEQRES 19 B 409 GLU GLU GLU PHE LYS ALA GLN PHE GLU ALA ALA GLY LEU SEQRES 20 B 409 THR TYR GLU HIS ARG LEU ILE ASP ASP MET VAL ALA ALA SEQRES 21 B 409 CYS LEU LYS TRP GLU GLY GLY TYR VAL TRP ALA CYS LYS SEQRES 22 B 409 ASN TYR ASP GLY ASP VAL GLN SER ASP THR VAL ALA GLN SEQRES 23 B 409 GLY TYR GLY SER LEU GLY LEU MET THR SER VAL LEU MET SEQRES 24 B 409 THR ALA ASP GLY LYS THR VAL GLU ALA GLU ALA ALA HIS SEQRES 25 B 409 GLY THR VAL THR ARG HIS TYR ARG GLN TYR GLN ALA GLY SEQRES 26 B 409 LYS PRO THR SER THR ASN PRO ILE ALA SER ILE PHE ALA SEQRES 27 B 409 TRP THR ARG GLY LEU GLN HIS ARG GLY LYS LEU ASP GLY SEQRES 28 B 409 THR PRO GLU VAL ILE ASP PHE ALA HIS LYS LEU GLU SER SEQRES 29 B 409 VAL VAL ILE ALA THR VAL GLU SER GLY LYS MET THR LYS SEQRES 30 B 409 ASP LEU ALA ILE LEU ILE GLY PRO GLU GLN ASP TRP LEU SEQRES 31 B 409 ASN SER GLU GLU PHE LEU ASP ALA ILE ALA ASP ASN LEU SEQRES 32 B 409 GLU LYS GLU LEU ALA ASN HET MN A 501 1 HET NDP A 502 48 HET CL A 503 1 HET MN B 501 1 HET NDP B 502 48 HET CL B 503 1 HETNAM MN MANGANESE (II) ION HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM CL CHLORIDE ION FORMUL 3 MN 2(MN 2+) FORMUL 4 NDP 2(C21 H30 N7 O17 P3) FORMUL 5 CL 2(CL 1-) FORMUL 9 HOH *310(H2 O) HELIX 1 1 ASP A 19 ILE A 34 1 16 HELIX 2 2 GLY A 48 THR A 55 1 8 HELIX 3 3 ASP A 57 GLY A 71 1 15 HELIX 4 4 ASP A 82 ASN A 90 1 9 HELIX 5 5 SER A 97 GLY A 107 1 11 HELIX 6 6 GLY A 139 ALA A 144 5 6 HELIX 7 7 LYS A 189 LYS A 207 1 19 HELIX 8 8 LEU A 219 PHE A 238 1 20 HELIX 9 9 PHE A 238 ALA A 244 1 7 HELIX 10 10 ILE A 254 TRP A 264 1 11 HELIX 11 11 LYS A 273 TYR A 288 1 16 HELIX 12 12 SER A 290 GLY A 292 5 3 HELIX 13 13 VAL A 315 GLY A 325 1 11 HELIX 14 14 PRO A 332 GLY A 351 1 20 HELIX 15 15 THR A 352 GLU A 371 1 20 HELIX 16 16 THR A 376 GLY A 384 1 9 HELIX 17 17 ASN A 391 LYS A 405 1 15 HELIX 18 18 ASP B 19 ILE B 34 1 16 HELIX 19 19 GLY B 48 THR B 55 1 8 HELIX 20 20 ASP B 57 GLY B 71 1 15 HELIX 21 21 ASP B 82 ASN B 90 1 9 HELIX 22 22 SER B 97 GLY B 107 1 11 HELIX 23 23 GLY B 139 ALA B 144 5 6 HELIX 24 24 LYS B 189 ALA B 206 1 18 HELIX 25 25 ALA B 221 PHE B 238 1 18 HELIX 26 26 PHE B 238 ALA B 245 1 8 HELIX 27 27 ILE B 254 TRP B 264 1 11 HELIX 28 28 LYS B 273 GLY B 289 1 17 HELIX 29 29 SER B 290 GLY B 292 5 3 HELIX 30 30 VAL B 315 ALA B 324 1 10 HELIX 31 31 PRO B 332 GLY B 351 1 20 HELIX 32 32 THR B 352 SER B 372 1 21 HELIX 33 33 THR B 376 GLY B 384 1 9 HELIX 34 34 ASN B 391 LYS B 405 1 15 SHEET 1 A 2 ILE A 7 LYS A 8 0 SHEET 2 A 2 LEU A 38 ASP A 39 1 O ASP A 39 N ILE A 7 SHEET 1 B10 LEU A 42 ASP A 46 0 SHEET 2 B10 VAL A 13 ASP A 17 1 N VAL A 13 O ASP A 43 SHEET 3 B10 VAL A 72 LYS A 75 1 O VAL A 74 N LEU A 16 SHEET 4 B10 VAL A 306 ALA A 310 1 O ALA A 308 N GLY A 73 SHEET 5 B10 MET A 294 MET A 299 -1 N LEU A 298 O GLU A 307 SHEET 6 B10 THR A 109 PRO A 114 -1 N GLU A 113 O THR A 295 SHEET 7 B10 ILE A 131 ARG A 135 -1 O ILE A 133 N ARG A 112 SHEET 8 B10 TYR A 268 CYS A 272 1 O TRP A 270 N VAL A 132 SHEET 9 B10 VAL A 210 THR A 214 1 N TYR A 211 O ALA A 271 SHEET 10 B10 TYR A 249 LEU A 253 1 O ARG A 252 N LEU A 212 SHEET 1 C 4 THR A 145 VAL A 149 0 SHEET 2 C 4 GLY A 180 PHE A 188 -1 O GLY A 184 N THR A 145 SHEET 3 C 4 GLY B 180 PHE B 188 -1 O LEU B 183 N MET A 185 SHEET 4 C 4 THR B 145 VAL B 149 -1 N THR B 145 O GLY B 184 SHEET 1 D 4 ILE A 168 ILE A 175 0 SHEET 2 D 4 GLY A 153 PRO A 161 -1 N LEU A 157 O HIS A 170 SHEET 3 D 4 GLY B 153 PRO B 161 -1 O THR B 154 N THR A 160 SHEET 4 D 4 ILE B 168 ILE B 175 -1 O ILE B 175 N GLY B 153 SHEET 1 E 2 ILE B 7 LYS B 8 0 SHEET 2 E 2 LEU B 38 ASP B 39 1 O ASP B 39 N ILE B 7 SHEET 1 F10 LEU B 42 ASP B 46 0 SHEET 2 F10 VAL B 13 ASP B 17 1 N ASP B 17 O TYR B 45 SHEET 3 F10 VAL B 72 LYS B 75 1 O VAL B 74 N LEU B 16 SHEET 4 F10 VAL B 306 GLU B 309 1 O ALA B 308 N LYS B 75 SHEET 5 F10 LEU B 298 MET B 299 -1 N LEU B 298 O GLU B 307 SHEET 6 F10 THR B 109 PRO B 114 -1 N THR B 109 O MET B 299 SHEET 7 F10 ILE B 131 ARG B 135 -1 O ILE B 133 N ARG B 112 SHEET 8 F10 TYR B 268 CYS B 272 1 O TRP B 270 N VAL B 132 SHEET 9 F10 VAL B 210 THR B 214 1 N TYR B 211 O ALA B 271 SHEET 10 F10 TYR B 249 LEU B 253 1 O ARG B 252 N LEU B 212 SHEET 1 G 7 LEU B 42 ASP B 46 0 SHEET 2 G 7 VAL B 13 ASP B 17 1 N ASP B 17 O TYR B 45 SHEET 3 G 7 VAL B 72 LYS B 75 1 O VAL B 74 N LEU B 16 SHEET 4 G 7 VAL B 306 GLU B 309 1 O ALA B 308 N LYS B 75 SHEET 5 G 7 LEU B 298 MET B 299 -1 N LEU B 298 O GLU B 307 SHEET 6 G 7 THR B 109 PRO B 114 -1 N THR B 109 O MET B 299 SHEET 7 G 7 MET B 294 THR B 295 -1 O THR B 295 N GLU B 113 LINK OD2 ASP A 255 MN MN B 501 1555 1555 2.30 LINK OD1 ASP A 278 MN MN A 501 1555 1555 2.20 LINK O ASP A 278 MN MN A 501 1555 1555 2.24 LINK OD2 ASP A 282 MN MN A 501 1555 1555 2.11 LINK MN MN A 501 O HOH A 708 1555 1555 2.47 LINK MN MN A 501 OD2 ASP B 255 1555 1555 2.16 LINK MN MN A 501 O HOH B 604 1555 1555 2.01 LINK O HOH A 607 MN MN B 501 1555 1555 2.12 LINK OD1 ASP B 278 MN MN B 501 1555 1555 2.15 LINK O ASP B 278 MN MN B 501 1555 1555 2.32 LINK OD2 ASP B 282 MN MN B 501 1555 1555 2.06 LINK MN MN B 501 O HOH B 720 1555 1555 2.73 CISPEP 1 SER A 296 VAL A 297 0 10.88 CISPEP 2 ASP A 302 GLY A 303 0 -10.23 CISPEP 3 ASP A 350 GLY A 351 0 -12.29 CISPEP 4 SER B 296 VAL B 297 0 21.10 CISPEP 5 ASP B 302 GLY B 303 0 -20.74 CISPEP 6 ASP B 350 GLY B 351 0 -16.78 SITE 1 AC1 5 ASP A 278 ASP A 282 HOH A 708 ASP B 255 SITE 2 AC1 5 HOH B 604 SITE 1 AC2 21 LYS A 75 ALA A 77 THR A 78 ILE A 79 SITE 2 AC2 21 THR A 80 ARG A 85 GLU A 309 HIS A 312 SITE 3 AC2 21 GLY A 313 THR A 314 VAL A 315 THR A 316 SITE 4 AC2 21 ARG A 317 HIS A 318 THR A 330 ASN A 331 SITE 5 AC2 21 HOH A 608 HOH A 610 HOH A 612 HOH A 724 SITE 6 AC2 21 HOH A 754 SITE 1 AC3 2 GLY A 139 ARG A 143 SITE 1 AC4 5 ASP A 255 HOH A 607 ASP B 278 ASP B 282 SITE 2 AC4 5 HOH B 720 SITE 1 AC5 19 LYS B 75 ALA B 77 THR B 78 THR B 80 SITE 2 AC5 19 ARG B 85 ASN B 99 GLU B 309 HIS B 312 SITE 3 AC5 19 GLY B 313 THR B 314 VAL B 315 THR B 316 SITE 4 AC5 19 HIS B 318 THR B 330 ASN B 331 HOH B 606 SITE 5 AC5 19 HOH B 686 HOH B 702 HOH B 707 SITE 1 AC6 4 PHE B 138 GLY B 139 ARG B 143 HOH B 658 CRYST1 90.135 92.704 102.894 90.00 90.00 90.00 P 21 21 21 8 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 0.011094 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009719 0.00000