HEADER OXIDOREDUCTASE 15-MAY-06 2CMV OBSLTE 27-JUN-18 2CMV 5YZI TITLE CRYSTAL STRUCTURE OF MOUSE CYTOSOLIC ISOCITRATE DEHYDROGENASE TITLE 2 COMPLEXED WITH CADMIUM AND CITRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 4-413; COMPND 5 SYNONYM: OXALOSUCCINATE DECARBOXYLASE, IDH, NADP, +-SPECIFIC ICDH), COMPND 6 IDP; COMPND 7 EC: 1.1.1.42; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRICARBOXYLIC ACID CYCLE, ISOCITRATE DEHYDROGENASE, NADP, CADMIUM, KEYWDS 2 OXIDOREDUCTASE, GLYOXYLATE BYPASS EXPDTA X-RAY DIFFRACTION AUTHOR H.J.CHO,K.J.KIM,T.L.HUH,B.S.KANG REVDAT 5 27-JUN-18 2CMV 1 OBSLTE REVDAT 4 28-MAR-18 2CMV 1 SOURCE REVDAT 3 13-JUL-11 2CMV 1 VERSN REVDAT 2 24-FEB-09 2CMV 1 VERSN REVDAT 1 29-MAY-07 2CMV 0 JRNL AUTH H.J.CHO,K.J.KIM,T.L.HUH,B.S.KANG JRNL TITL CRYSTAL STRUCTURE OF MOUSE CYTOSOLIC ISOCITRATE JRNL TITL 2 DEHYDROGENASE COMPLEXED WITH CADMIUM AND CITRATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 27771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1476 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.52 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1798 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6435 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 124 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.22000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : 0.54000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.53000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.128 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.305 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.231 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.105 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6693 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9054 ; 1.340 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 817 ; 6.096 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 301 ;36.513 ;24.817 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1172 ;16.445 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;22.043 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 981 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5008 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3103 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4597 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 326 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 28 ; 0.193 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.077 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4169 ; 0.487 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6522 ; 0.776 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2900 ; 1.265 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2532 ; 1.988 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 413 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2700 -0.0250 31.8030 REMARK 3 T TENSOR REMARK 3 T11: -0.0498 T22: -0.1148 REMARK 3 T33: -0.2425 T12: 0.0350 REMARK 3 T13: -0.0781 T23: 0.0384 REMARK 3 L TENSOR REMARK 3 L11: 1.7343 L22: 0.7657 REMARK 3 L33: 2.5156 L12: 0.4643 REMARK 3 L13: -0.2430 L23: 0.3091 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: -0.0824 S13: 0.0032 REMARK 3 S21: 0.0581 S22: -0.0373 S23: 0.0766 REMARK 3 S31: 0.2117 S32: -0.1398 S33: 0.0365 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 413 REMARK 3 ORIGIN FOR THE GROUP (A): 20.5230 -3.1440 16.8870 REMARK 3 T TENSOR REMARK 3 T11: -0.0942 T22: 0.2778 REMARK 3 T33: -0.2667 T12: 0.1348 REMARK 3 T13: -0.0807 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 1.1673 L22: 0.6970 REMARK 3 L33: 2.9676 L12: -0.2803 REMARK 3 L13: -0.3286 L23: 0.5850 REMARK 3 S TENSOR REMARK 3 S11: -0.0317 S12: 0.0313 S13: -0.0265 REMARK 3 S21: -0.0442 S22: 0.1287 S23: -0.0578 REMARK 3 S31: 0.2298 S32: 1.0913 S33: -0.0970 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2CMV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1290028733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29260 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.03000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2CMJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 49.12300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.71400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.12300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.71400 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: PQS 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 LYS B 413 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 LYS A 87 CG CD CE NZ REMARK 470 LYS A 233 CD CE NZ REMARK 470 LYS B 58 CD CE NZ REMARK 470 LYS B 65 CG CD CE NZ REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 GLU B 80 CD OE1 OE2 REMARK 470 LYS B 81 CD CE NZ REMARK 470 GLU B 84 CG CD OE1 OE2 REMARK 470 LYS B 233 CD CE NZ REMARK 470 LYS B 301 CD CE NZ REMARK 470 GLN B 323 CD OE1 NE2 REMARK 470 LYS B 381 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 O ILE B 99 O HOH B 2010 1.73 REMARK 500 OB1 FLC B 1416 O HOH B 2048 1.87 REMARK 500 N LEU B 103 O HOH B 2010 2.03 REMARK 500 NH1 ARG B 49 O HOH B 2004 2.09 REMARK 500 OG SER A 94 OG1 FLC A 1416 2.13 REMARK 500 OG SER B 94 OG2 FLC B 1416 2.17 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 17 -127.10 36.00 REMARK 500 ILE A 31 -66.09 -121.32 REMARK 500 ASN A 68 -11.01 77.90 REMARK 500 ASP A 79 -161.99 -104.83 REMARK 500 ASP A 137 -139.12 47.87 REMARK 500 ARG A 140 49.02 -148.33 REMARK 500 ASP A 160 26.54 -74.21 REMARK 500 THR A 162 -167.53 -58.01 REMARK 500 LYS A 212 56.24 -116.33 REMARK 500 LEU A 216 73.01 -108.87 REMARK 500 ASN A 243 57.00 79.40 REMARK 500 VAL A 312 44.35 79.94 REMARK 500 ASN A 348 38.77 32.73 REMARK 500 ALA A 412 30.29 -71.78 REMARK 500 GLU B 17 -140.82 44.04 REMARK 500 ILE B 21 -70.24 -62.75 REMARK 500 ASN B 68 -6.58 77.46 REMARK 500 LYS B 89 -76.81 -58.75 REMARK 500 ASP B 137 -138.13 51.78 REMARK 500 ASP B 252 -71.93 -41.08 REMARK 500 MET B 290 67.35 -110.47 REMARK 500 LYS B 301 -38.25 -140.31 REMARK 500 ALA B 308 -47.21 62.79 REMARK 500 SER B 326 96.28 -165.30 REMARK 500 ASN B 348 14.90 46.27 REMARK 500 GLN B 411 9.51 -54.66 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 CD A1414 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 279 OD2 REMARK 620 2 FLC A1416 OA1 142.1 REMARK 620 3 HOH A2022 O 60.0 82.3 REMARK 620 4 HOH A2051 O 70.5 97.2 73.0 REMARK 620 5 ASP A 275 OD2 117.5 77.9 112.8 171.5 REMARK 620 6 ASP B 252 OD2 117.4 96.7 159.4 86.8 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B1414 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 275 OD2 REMARK 620 2 FLC B1416 OA2 88.8 REMARK 620 3 ASP A 252 OD1 69.2 102.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A1414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC A1416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B1414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC B1416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A1415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP B1415 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CMJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MOUSE CYTOSOLIC ISOCITRATE DEHYDROGENASE DBREF 2CMV A 4 413 UNP O88844 IDHC_MOUSE 4 413 DBREF 2CMV B 4 413 UNP O88844 IDHC_MOUSE 4 413 SEQRES 1 A 410 LYS ILE GLN GLY GLY SER VAL VAL GLU MET GLN GLY ASP SEQRES 2 A 410 GLU MET THR ARG ILE ILE TRP GLU LEU ILE LYS GLU LYS SEQRES 3 A 410 LEU ILE LEU PRO TYR VAL GLU LEU ASP LEU HIS SER TYR SEQRES 4 A 410 ASP LEU GLY ILE GLU ASN ARG ASP ALA THR ASN ASP GLN SEQRES 5 A 410 VAL THR LYS ASP ALA ALA GLU ALA ILE LYS LYS TYR ASN SEQRES 6 A 410 VAL GLY VAL LYS CYS ALA THR ILE THR PRO ASP GLU LYS SEQRES 7 A 410 ARG VAL GLU GLU PHE LYS LEU LYS GLN MET TRP LYS SER SEQRES 8 A 410 PRO ASN GLY THR ILE ARG ASN ILE LEU GLY GLY THR VAL SEQRES 9 A 410 PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE PRO ARG LEU SEQRES 10 A 410 VAL THR GLY TRP VAL LYS PRO ILE ILE ILE GLY ARG HIS SEQRES 11 A 410 ALA TYR GLY ASP GLN TYR ARG ALA THR ASP PHE VAL VAL SEQRES 12 A 410 PRO GLY PRO GLY LYS VAL GLU ILE THR TYR THR PRO LYS SEQRES 13 A 410 ASP GLY THR GLN LYS VAL THR TYR MET VAL HIS ASP PHE SEQRES 14 A 410 GLU GLU GLY GLY GLY VAL ALA MET GLY MET TYR ASN GLN SEQRES 15 A 410 ASP LYS SER ILE GLU ASP PHE ALA HIS SER SER PHE GLN SEQRES 16 A 410 MET ALA LEU SER LYS GLY TRP PRO LEU TYR LEU SER THR SEQRES 17 A 410 LYS ASN THR ILE LEU LYS LYS TYR ASP GLY ARG PHE LYS SEQRES 18 A 410 ASP ILE PHE GLN GLU ILE TYR ASP LYS LYS TYR LYS SER SEQRES 19 A 410 GLN PHE GLU ALA GLN ASN ILE CYS TYR GLU HIS ARG LEU SEQRES 20 A 410 ILE ASP ASP MET VAL ALA GLN ALA MET LYS SER GLU GLY SEQRES 21 A 410 GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP GLY ASP VAL SEQRES 22 A 410 GLN SER ASP SER VAL ALA GLN GLY TYR GLY SER LEU GLY SEQRES 23 A 410 MET MET THR SER VAL LEU ILE CYS PRO ASP GLY LYS THR SEQRES 24 A 410 VAL GLU ALA GLU ALA ALA HIS GLY THR VAL THR ARG HIS SEQRES 25 A 410 TYR ARG MET TYR GLN LYS GLY GLN GLU THR SER THR ASN SEQRES 26 A 410 PRO ILE ALA SER ILE PHE ALA TRP SER ARG GLY LEU ALA SEQRES 27 A 410 HIS ARG ALA LYS LEU ASP ASN ASN THR GLU LEU SER PHE SEQRES 28 A 410 PHE ALA LYS ALA LEU GLU ASP VAL CYS ILE GLU THR ILE SEQRES 29 A 410 GLU ALA GLY PHE MET THR LYS ASP LEU ALA ALA CYS ILE SEQRES 30 A 410 LYS GLY LEU PRO ASN VAL GLN ARG SER ASP TYR LEU ASN SEQRES 31 A 410 THR PHE GLU PHE MET ASP LYS LEU GLY GLU ASN LEU LYS SEQRES 32 A 410 ALA LYS LEU ALA GLN ALA LYS SEQRES 1 B 410 LYS ILE GLN GLY GLY SER VAL VAL GLU MET GLN GLY ASP SEQRES 2 B 410 GLU MET THR ARG ILE ILE TRP GLU LEU ILE LYS GLU LYS SEQRES 3 B 410 LEU ILE LEU PRO TYR VAL GLU LEU ASP LEU HIS SER TYR SEQRES 4 B 410 ASP LEU GLY ILE GLU ASN ARG ASP ALA THR ASN ASP GLN SEQRES 5 B 410 VAL THR LYS ASP ALA ALA GLU ALA ILE LYS LYS TYR ASN SEQRES 6 B 410 VAL GLY VAL LYS CYS ALA THR ILE THR PRO ASP GLU LYS SEQRES 7 B 410 ARG VAL GLU GLU PHE LYS LEU LYS GLN MET TRP LYS SER SEQRES 8 B 410 PRO ASN GLY THR ILE ARG ASN ILE LEU GLY GLY THR VAL SEQRES 9 B 410 PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE PRO ARG LEU SEQRES 10 B 410 VAL THR GLY TRP VAL LYS PRO ILE ILE ILE GLY ARG HIS SEQRES 11 B 410 ALA TYR GLY ASP GLN TYR ARG ALA THR ASP PHE VAL VAL SEQRES 12 B 410 PRO GLY PRO GLY LYS VAL GLU ILE THR TYR THR PRO LYS SEQRES 13 B 410 ASP GLY THR GLN LYS VAL THR TYR MET VAL HIS ASP PHE SEQRES 14 B 410 GLU GLU GLY GLY GLY VAL ALA MET GLY MET TYR ASN GLN SEQRES 15 B 410 ASP LYS SER ILE GLU ASP PHE ALA HIS SER SER PHE GLN SEQRES 16 B 410 MET ALA LEU SER LYS GLY TRP PRO LEU TYR LEU SER THR SEQRES 17 B 410 LYS ASN THR ILE LEU LYS LYS TYR ASP GLY ARG PHE LYS SEQRES 18 B 410 ASP ILE PHE GLN GLU ILE TYR ASP LYS LYS TYR LYS SER SEQRES 19 B 410 GLN PHE GLU ALA GLN ASN ILE CYS TYR GLU HIS ARG LEU SEQRES 20 B 410 ILE ASP ASP MET VAL ALA GLN ALA MET LYS SER GLU GLY SEQRES 21 B 410 GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP GLY ASP VAL SEQRES 22 B 410 GLN SER ASP SER VAL ALA GLN GLY TYR GLY SER LEU GLY SEQRES 23 B 410 MET MET THR SER VAL LEU ILE CYS PRO ASP GLY LYS THR SEQRES 24 B 410 VAL GLU ALA GLU ALA ALA HIS GLY THR VAL THR ARG HIS SEQRES 25 B 410 TYR ARG MET TYR GLN LYS GLY GLN GLU THR SER THR ASN SEQRES 26 B 410 PRO ILE ALA SER ILE PHE ALA TRP SER ARG GLY LEU ALA SEQRES 27 B 410 HIS ARG ALA LYS LEU ASP ASN ASN THR GLU LEU SER PHE SEQRES 28 B 410 PHE ALA LYS ALA LEU GLU ASP VAL CYS ILE GLU THR ILE SEQRES 29 B 410 GLU ALA GLY PHE MET THR LYS ASP LEU ALA ALA CYS ILE SEQRES 30 B 410 LYS GLY LEU PRO ASN VAL GLN ARG SER ASP TYR LEU ASN SEQRES 31 B 410 THR PHE GLU PHE MET ASP LYS LEU GLY GLU ASN LEU LYS SEQRES 32 B 410 ALA LYS LEU ALA GLN ALA LYS HET CD A1414 1 HET NAP A1415 48 HET FLC A1416 13 HET CD B1414 1 HET NAP B1415 48 HET FLC B1416 13 HETNAM CD CADMIUM ION HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM FLC CITRATE ANION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 CD 2(CD 2+) FORMUL 4 NAP 2(C21 H28 N7 O17 P3) FORMUL 5 FLC 2(C6 H5 O7 3-) FORMUL 9 HOH *116(H2 O) HELIX 1 1 ASP A 16 ILE A 31 1 16 HELIX 2 2 GLY A 45 THR A 52 1 8 HELIX 3 3 ASP A 54 ASN A 68 1 15 HELIX 4 4 ASP A 79 LYS A 87 1 9 HELIX 5 5 SER A 94 GLY A 104 1 11 HELIX 6 6 GLY A 136 ALA A 141 5 6 HELIX 7 7 ASP A 186 GLY A 204 1 19 HELIX 8 8 LYS A 218 TYR A 235 1 18 HELIX 9 9 TYR A 235 ASN A 243 1 9 HELIX 10 10 ILE A 251 SER A 261 1 11 HELIX 11 11 LYS A 270 GLY A 286 1 17 HELIX 12 12 VAL A 312 LYS A 321 1 10 HELIX 13 13 PRO A 329 ASP A 347 1 19 HELIX 14 14 ASN A 349 ALA A 369 1 21 HELIX 15 15 THR A 373 GLY A 382 1 10 HELIX 16 16 GLN A 387 TYR A 391 5 5 HELIX 17 17 ASN A 393 ALA A 412 1 20 HELIX 18 18 ASP B 16 ILE B 31 1 16 HELIX 19 19 GLY B 45 THR B 52 1 8 HELIX 20 20 ASP B 54 ASN B 68 1 15 HELIX 21 21 ASP B 79 LYS B 87 1 9 HELIX 22 22 SER B 94 GLY B 104 1 11 HELIX 23 23 GLY B 136 ALA B 141 5 6 HELIX 24 24 ASP B 186 GLY B 204 1 19 HELIX 25 25 LYS B 218 TYR B 235 1 18 HELIX 26 26 TYR B 235 GLN B 242 1 8 HELIX 27 27 ILE B 251 LYS B 260 1 10 HELIX 28 28 LYS B 270 GLY B 286 1 17 HELIX 29 29 VAL B 312 LYS B 321 1 10 HELIX 30 30 PRO B 329 ASN B 348 1 20 HELIX 31 31 ASN B 349 ALA B 369 1 21 HELIX 32 32 THR B 373 GLY B 382 1 10 HELIX 33 33 LEU B 383 VAL B 386 5 4 HELIX 34 34 GLN B 387 TYR B 391 5 5 HELIX 35 35 ASN B 393 GLN B 411 1 19 SHEET 1 AA10 VAL A 35 ASP A 43 0 SHEET 2 AA10 ILE A 5 GLN A 14 1 O ILE A 5 N GLU A 36 SHEET 3 AA10 VAL A 69 LYS A 72 1 O VAL A 69 N VAL A 11 SHEET 4 AA10 VAL A 303 GLU A 306 1 O VAL A 303 N GLY A 70 SHEET 5 AA10 MET A 291 ILE A 296 -1 O SER A 293 N GLU A 306 SHEET 6 AA10 THR A 106 ALA A 111 -1 O THR A 106 N ILE A 296 SHEET 7 AA10 ILE A 128 HIS A 133 -1 O ILE A 130 N ARG A 109 SHEET 8 AA10 PHE A 265 CYS A 269 1 O PHE A 265 N ILE A 129 SHEET 9 AA10 LEU A 207 THR A 211 1 O TYR A 208 N ALA A 268 SHEET 10 AA10 TYR A 246 LEU A 250 1 O GLU A 247 N LEU A 209 SHEET 1 AB 4 THR A 142 VAL A 146 0 SHEET 2 AB 4 GLY A 177 GLN A 185 -1 O GLY A 177 N VAL A 146 SHEET 3 AB 4 GLY B 177 GLN B 185 -1 O VAL B 178 N ASN A 184 SHEET 4 AB 4 THR B 142 VAL B 146 -1 O THR B 142 N GLY B 181 SHEET 1 AC 4 VAL A 165 PHE A 172 0 SHEET 2 AC 4 GLY A 150 PRO A 158 -1 O GLY A 150 N PHE A 172 SHEET 3 AC 4 GLY B 150 PRO B 158 -1 O LYS B 151 N THR A 157 SHEET 4 AC 4 VAL B 165 PHE B 172 -1 O VAL B 165 N TYR B 156 SHEET 1 BA10 VAL B 35 HIS B 40 0 SHEET 2 BA10 ILE B 5 MET B 13 1 O ILE B 5 N GLU B 36 SHEET 3 BA10 VAL B 69 LYS B 72 1 O VAL B 69 N VAL B 11 SHEET 4 BA10 VAL B 303 ALA B 305 1 O VAL B 303 N GLY B 70 SHEET 5 BA10 MET B 291 ILE B 296 -1 O LEU B 295 N GLU B 304 SHEET 6 BA10 THR B 106 ALA B 111 -1 O THR B 106 N ILE B 296 SHEET 7 BA10 ILE B 128 HIS B 133 -1 O ILE B 128 N ALA B 111 SHEET 8 BA10 PHE B 265 CYS B 269 1 O PHE B 265 N ILE B 129 SHEET 9 BA10 LEU B 207 THR B 211 1 O TYR B 208 N ALA B 268 SHEET 10 BA10 TYR B 246 LEU B 250 1 O GLU B 247 N LEU B 209 LINK CD CD A1414 OD2 ASP A 279 1555 1555 3.11 LINK CD CD A1414 OA1 FLC A1416 1555 1555 2.22 LINK CD CD A1414 O HOH A2022 1555 1555 2.30 LINK CD CD A1414 O HOH A2051 1555 1555 2.29 LINK CD CD A1414 OD2 ASP A 275 1555 1555 1.97 LINK CD CD A1414 OD2 ASP B 252 1555 1555 2.08 LINK CD CD B1414 OD2 ASP B 275 1555 1555 2.46 LINK CD CD B1414 OA2 FLC B1416 1555 1555 1.94 LINK CD CD B1414 OD1 ASP A 252 1555 1555 2.57 SITE 1 AC1 6 ASP A 275 ASP A 279 FLC A1416 HOH A2022 SITE 2 AC1 6 HOH A2051 ASP B 252 SITE 1 AC2 14 THR A 77 SER A 94 ASN A 96 ARG A 100 SITE 2 AC2 14 ARG A 109 ARG A 132 TYR A 139 ASP A 275 SITE 3 AC2 14 CD A1414 NAP A1415 HOH A2022 LYS B 212 SITE 4 AC2 14 ILE B 215 ASP B 252 SITE 1 AC3 4 ASP A 252 ASP B 275 ASP B 279 FLC B1416 SITE 1 AC4 15 LYS A 212 ILE A 215 ASP A 252 THR B 77 SITE 2 AC4 15 SER B 94 ASN B 96 ARG B 100 ARG B 109 SITE 3 AC4 15 ARG B 132 TYR B 139 ASP B 275 ALA B 308 SITE 4 AC4 15 CD B1414 NAP B1415 HOH B2048 SITE 1 AC5 24 LYS A 72 ALA A 74 THR A 75 THR A 77 SITE 2 AC5 24 ARG A 82 ASN A 96 HIS A 309 GLY A 310 SITE 3 AC5 24 THR A 311 VAL A 312 THR A 313 ARG A 314 SITE 4 AC5 24 HIS A 315 ASN A 328 FLC A1416 HOH A2064 SITE 5 AC5 24 HOH A2065 HOH A2066 HOH A2067 HOH A2068 SITE 6 AC5 24 ASP B 253 GLN B 257 LYS B 260 HOH B2032 SITE 1 AC6 17 LYS A 260 LYS B 72 ALA B 74 THR B 75 SITE 2 AC6 17 THR B 77 ASN B 96 LEU B 288 GLU B 306 SITE 3 AC6 17 HIS B 309 GLY B 310 THR B 311 VAL B 312 SITE 4 AC6 17 THR B 313 ARG B 314 ASN B 328 FLC B1416 SITE 5 AC6 17 HOH B2047 CRYST1 98.246 91.428 109.724 90.00 113.65 90.00 C 1 2 1 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 0.010179 0.000000 0.004457 0.00000 SCALE2 0.000000 0.010938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009949 0.00000