HEADER OXIDOREDUCTASE 30-MAR-12 4AOU TITLE CTIDH BOUND TO NADP. THE COMPLEX STRUCTURES OF ISOCITRATE TITLE 2 DEHYDROGENASE FROM CLOSTRIDIUM THERMOCELLUM AND DESULFOTALEA TITLE 3 PSYCHROPHILA, SUPPORT A NEW ACTIVE SITE LOCKING MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP]; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.42; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM THERMOCELLUM; SOURCE 3 ORGANISM_TAXID: 1515; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, TEMPERATURE ADAPTATION, THERMOPHILIC, PSYCHROPHILIC, KEYWDS 2 NADP+ SELECTIVITY, DOMAIN MOVEMENTS EXPDTA X-RAY DIFFRACTION AUTHOR H.-K.S.LEIROS,A.-E.FEDOY,I.LEIROS,I.H.STEEN REVDAT 6 08-MAY-24 4AOU 1 REMARK LINK REVDAT 5 15-MAY-19 4AOU 1 JRNL REMARK REVDAT 4 08-MAY-19 4AOU 1 REMARK REVDAT 3 22-MAY-13 4AOU 1 JRNL REVDAT 2 20-MAR-13 4AOU 1 JRNL REVDAT 1 11-JUL-12 4AOU 0 JRNL AUTH H.K.LEIROS,A.E.FEDOY,I.LEIROS,I.H.STEEN JRNL TITL THE COMPLEX STRUCTURES OF ISOCITRATE DEHYDROGENASE FROM JRNL TITL 2 CLOSTRIDIUM THERMOCELLUM AND DESULFOTALEA PSYCHROPHILA JRNL TITL 3 SUGGEST A NEW ACTIVE SITE LOCKING MECHANISM. JRNL REF FEBS OPEN BIO V. 2 159 2012 JRNL REFN ESSN 2211-5463 JRNL PMID 23650595 JRNL DOI 10.1016/J.FOB.2012.06.003 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0069 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19347 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1043 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1385 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3210 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -1.07000 REMARK 3 B12 (A**2) : 0.36000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.349 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.256 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.724 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3299 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4465 ; 1.883 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 7.143 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;36.071 ;24.392 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 579 ;19.670 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;20.890 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 491 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2453 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1991 ; 0.788 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3216 ; 1.509 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1308 ; 2.406 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1249 ; 3.757 ; 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 : NULL 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 4AOU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1290051916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91840 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20411 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.0000 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) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP METHOD. RESERVOIR REMARK 280 SOLUTIONS OF 9-11% (W/V) POLYETHYLENE GLYCOL (PEG) PEG3350, AND REMARK 280 0.15 M AMMONIUM DIHYDROGEN CITRATE, 10% (V/V/) PROPYLENE GLYCOL REMARK 280 AT 37 DEG. C. CTIDH-NADP AT 5 MG/ML, 10 MM NADP AND 10 MM DL- REMARK 280 ISOCITRATE., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.39333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.19667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.19667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 40.39333 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: 11620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.4 KCAL/MOL 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -40.39333 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 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 GLU A 36 CG CD OE1 OE2 REMARK 480 GLU A 84 CD OE1 OE2 REMARK 480 ASN A 115 OD1 REMARK 480 LYS A 125 CE NZ REMARK 480 LYS A 126 CD CE NZ REMARK 480 GLU A 162 CD OE1 OE2 REMARK 480 LYS A 185 CE NZ REMARK 480 GLN A 243 NE2 REMARK 480 LYS A 339 CE NZ REMARK 480 LYS A 347 CG CD CE NZ REMARK 480 LYS A 371 CD CE REMARK 480 LYS A 392 CD CE 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 OG SER A 116 OE1 GLU A 365 2.14 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 GLU A 84 CG GLU A 84 CD -0.090 REMARK 500 GLU A 162 CG GLU A 162 CD -0.379 REMARK 500 LYS A 185 CD LYS A 185 CE -0.205 REMARK 500 GLN A 243 CD GLN A 243 NE2 0.218 REMARK 500 LYS A 371 CE LYS A 371 NZ -0.652 REMARK 500 LYS A 392 CG LYS A 392 CD -0.436 REMARK 500 LYS A 392 CE LYS A 392 NZ -0.499 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 PRO A 33 C - N - CA ANGL. DEV. = -9.7 DEGREES REMARK 500 GLN A 243 OE1 - CD - NE2 ANGL. DEV. = -23.5 DEGREES REMARK 500 VAL A 253 CB - CA - C ANGL. DEV. = -12.0 DEGREES REMARK 500 LYS A 347 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 LYS A 371 CB - CG - CD ANGL. DEV. = 46.9 DEGREES REMARK 500 LYS A 392 CB - CG - CD ANGL. DEV. = 30.6 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 LYS A 7 -95.95 -94.82 REMARK 500 GLU A 17 -128.79 47.77 REMARK 500 LEU A 31 -71.19 -112.92 REMARK 500 ASP A 54 -0.60 66.16 REMARK 500 ASP A 104 166.00 56.87 REMARK 500 ASP A 137 -138.62 53.60 REMARK 500 SER A 148 -167.01 -164.66 REMARK 500 ALA A 149 150.61 -46.23 REMARK 500 ASN A 160 -118.47 -72.79 REMARK 500 ASP A 200 -36.93 -39.05 REMARK 500 LYS A 210 67.94 -118.75 REMARK 500 TYR A 217 -74.06 -46.57 REMARK 500 GLU A 232 -18.96 -163.61 REMARK 500 MET A 288 57.78 -96.20 REMARK 500 LYS A 318 3.14 -67.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN A 243 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 NAP A 1520 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 MG A1404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 250 OD2 REMARK 620 2 ASP A 273 OD1 87.4 REMARK 620 3 ICT A1403 O1 164.0 82.7 REMARK 620 4 ICT A1403 O7 84.1 89.3 83.3 REMARK 620 5 HOH A2029 O 100.6 81.2 90.3 169.2 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 NAP A 1520 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AOV RELATED DB: PDB REMARK 900 DPIDH-NADP. THE COMPLEX STRUCTURES OF ISOCITRATE DEHYDROGENASE FROM REMARK 900 CLOSTRIDIUM THERMOCELLUM AND DESULFOTALEA PSYCHROPHILA, SUPPORT A REMARK 900 NEW ACTIVE SITE LOCKING MECHANISM DBREF 4AOU A 1 402 UNP A3DC45 A3DC45_CLOTH 1 402 SEQRES 1 A 402 MET SER LYS ILE LYS MET LYS VAL PRO LEU VAL GLU MET SEQRES 2 A 402 ASP GLY ASP GLU MET THR ARG ILE ILE TRP ARG LEU ILE SEQRES 3 A 402 LYS GLU ASN LEU LEU GLU PRO TYR ILE GLU LEU ASN THR SEQRES 4 A 402 GLU TYR TYR ASP LEU GLY LEU GLU ASN ARG ASP LYS THR SEQRES 5 A 402 GLU ASP GLN VAL THR ILE ASP ALA ALA ARG ALA ILE GLN SEQRES 6 A 402 LYS TYR GLY VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 A 402 ASN ALA GLN ARG VAL GLU GLU TYR ASN LEU LYS LYS MET SEQRES 8 A 402 TRP LYS SER PRO ASN GLY THR ILE ARG ALA ILE LEU ASP SEQRES 9 A 402 GLY THR VAL PHE ARG ALA PRO ILE VAL VAL ASN SER ILE SEQRES 10 A 402 LYS PRO PHE VAL LYS GLY TRP LYS LYS PRO ILE SER ILE SEQRES 11 A 402 ALA ARG HIS ALA TYR GLY ASP VAL TYR LYS ASN VAL GLU SEQRES 12 A 402 TYR TYR VAL PRO SER ALA GLY LYS ALA GLU LEU VAL PHE SEQRES 13 A 402 THR SER GLU ASN GLY GLU VAL SER ARG GLN THR ILE HIS SEQRES 14 A 402 GLU PHE ASP GLY PRO GLY VAL ILE MET GLY MET HIS ASN SEQRES 15 A 402 THR ASP LYS SER ILE ARG SER PHE ALA ARG ALA CYS PHE SEQRES 16 A 402 ASN TYR ALA LEU ASP MET ASN GLN ASP LEU TRP PHE SER SEQRES 17 A 402 THR LYS ASP THR ILE SER LYS THR TYR ASP HIS ARG PHE SEQRES 18 A 402 LYS ASP ILE PHE GLN GLU ILE TYR GLU ASN GLU TYR LYS SEQRES 19 A 402 GLU LYS PHE GLU ALA LYS ASN LEU GLN TYR PHE TYR THR SEQRES 20 A 402 LEU ILE ASP ASP ALA VAL ALA ARG ILE ILE ARG SER GLU SEQRES 21 A 402 GLY GLY MET VAL TRP ALA CYS LYS ASN TYR ASP GLY ASP SEQRES 22 A 402 VAL MET SER ASP MET VAL ALA SER ALA PHE GLY SER LEU SEQRES 23 A 402 ALA MET MET THR SER VAL LEU VAL SER PRO ASP GLY LYS SEQRES 24 A 402 TYR GLU PHE GLU ALA ALA HIS GLY THR VAL THR ARG HIS SEQRES 25 A 402 TYR TYR LYS HIS LEU LYS GLY GLU GLU THR SER THR ASN SEQRES 26 A 402 SER MET ALA THR ILE PHE ALA TRP THR GLY ALA LEU LYS SEQRES 27 A 402 LYS ARG GLY GLU LEU ASP GLY ILE LYS GLU LEU VAL ASP SEQRES 28 A 402 PHE ALA THR LYS LEU GLU GLN ALA SER VAL GLN THR ILE SEQRES 29 A 402 GLU ASN GLY VAL MET THR LYS ASP LEU ALA SER LEU SER SEQRES 30 A 402 GLU VAL PRO GLU LYS LYS ILE VAL ASN THR GLU ASP PHE SEQRES 31 A 402 LEU LYS GLU ILE ARG LYS THR PHE GLU GLY MET ALA HET ICT A1403 13 HET MG A1404 1 HET NAP A1520 48 HETNAM ICT ISOCITRIC ACID HETNAM MG MAGNESIUM ION HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 ICT C6 H8 O7 FORMUL 3 MG MG 2+ FORMUL 4 NAP C21 H28 N7 O17 P3 FORMUL 5 HOH *41(H2 O) HELIX 1 1 ASP A 16 LEU A 31 1 16 HELIX 2 2 GLY A 45 THR A 52 1 8 HELIX 3 3 ASP A 54 GLY A 68 1 15 HELIX 4 4 ASN A 79 ASN A 87 1 9 HELIX 5 5 SER A 94 ASP A 104 1 11 HELIX 6 6 GLY A 136 ASN A 141 5 6 HELIX 7 7 THR A 183 ASN A 202 1 20 HELIX 8 8 THR A 216 ASN A 231 1 16 HELIX 9 9 TYR A 233 LYS A 240 1 8 HELIX 10 10 ILE A 249 SER A 259 1 11 HELIX 11 11 LYS A 268 GLY A 284 1 17 HELIX 12 12 VAL A 309 LYS A 318 1 10 HELIX 13 13 SER A 326 GLY A 345 1 20 HELIX 14 14 ILE A 346 ASN A 366 1 21 HELIX 15 15 THR A 370 SER A 375 1 6 HELIX 16 16 ASN A 386 GLY A 400 1 15 SHEET 1 AA10 THR A 39 ASP A 43 0 SHEET 2 AA10 LEU A 10 ASP A 14 1 O LEU A 10 N GLU A 40 SHEET 3 AA10 VAL A 69 LYS A 72 1 O VAL A 69 N VAL A 11 SHEET 4 AA10 TYR A 300 ALA A 304 1 O TYR A 300 N GLY A 70 SHEET 5 AA10 MET A 289 VAL A 294 -1 O SER A 291 N GLU A 303 SHEET 6 AA10 THR A 106 PRO A 111 -1 O THR A 106 N VAL A 294 SHEET 7 AA10 SER A 129 HIS A 133 -1 O ILE A 130 N ARG A 109 SHEET 8 AA10 VAL A 264 CYS A 267 1 O TRP A 265 N ALA A 131 SHEET 9 AA10 LEU A 205 THR A 209 1 O TRP A 206 N ALA A 266 SHEET 10 AA10 TYR A 244 LEU A 248 1 O PHE A 245 N PHE A 207 SHEET 1 AB 2 VAL A 142 VAL A 146 0 SHEET 2 AB 2 GLY A 175 GLY A 179 -1 O GLY A 175 N VAL A 146 SHEET 1 AC 2 GLY A 150 THR A 157 0 SHEET 2 AC 2 VAL A 163 PHE A 171 -1 O SER A 164 N PHE A 156 SHEET 1 AD 2 VAL A 368 MET A 369 0 SHEET 2 AD 2 LYS A 383 ILE A 384 1 O LYS A 383 N MET A 369 LINK OD2 ASP A 250 MG MG A1404 5554 1555 2.15 LINK OD1 ASP A 273 MG MG A1404 1555 1555 2.04 LINK O1 ICT A1403 MG MG A1404 1555 1555 2.12 LINK O7 ICT A1403 MG MG A1404 1555 1555 2.19 LINK MG MG A1404 O HOH A2029 1555 1555 1.95 SITE 1 AC1 18 THR A 75 THR A 77 ARG A 82 ASP A 251 SITE 2 AC1 18 ARG A 255 LEU A 286 ALA A 287 HIS A 306 SITE 3 AC1 18 GLY A 307 THR A 308 VAL A 309 THR A 310 SITE 4 AC1 18 ARG A 311 HIS A 312 ASN A 325 ICT A1403 SITE 5 AC1 18 HOH A2032 HOH A2040 SITE 1 AC2 15 THR A 77 SER A 94 ASN A 96 ARG A 100 SITE 2 AC2 15 ARG A 109 ARG A 132 TYR A 139 LYS A 210 SITE 3 AC2 15 ILE A 213 ASP A 250 ASP A 273 ALA A 305 SITE 4 AC2 15 MG A1404 NAP A1520 HOH A2029 SITE 1 AC3 4 ASP A 250 ASP A 273 ICT A1403 HOH A2029 CRYST1 129.200 129.200 60.590 90.00 90.00 120.00 P 32 2 1 6 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 0.007740 0.004469 0.000000 0.00000 SCALE2 0.000000 0.008937 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016504 0.00000