HEADER OXIDOREDUCTASE 16-FEB-12 4AJA TITLE 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE IN COMPLEX WITH TITLE 2 ISOCITRATE, CALCIUM(II) AND THIONADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADP ISOCITRATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.42; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, OXIDATIVE BETA-DECARBOXYLATION EXPDTA X-RAY DIFFRACTION AUTHOR S.GONCALVES,S.P.MILLER,M.A.CARRONDO,A.M.DEAN,P.M.MATIAS REVDAT 2 20-DEC-23 4AJA 1 REMARK LINK REVDAT 1 31-OCT-12 4AJA 0 JRNL AUTH S.GONCALVES,S.P.MILLER,M.A.CARRONDO,A.M.DEAN,P.M.MATIAS JRNL TITL INDUCED FIT AND THE CATALYTIC MECHANISM OF ISOCITRATE JRNL TITL 2 DEHYDROGENASE. JRNL REF BIOCHEMISTRY V. 51 7098 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22891681 JRNL DOI 10.1021/BI300483W REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 76173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3802 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 46.5302 - 3.8752 1.00 7670 406 0.1489 0.1611 REMARK 3 2 3.8752 - 3.0761 1.00 7360 399 0.1614 0.1781 REMARK 3 3 3.0761 - 2.6873 1.00 7281 393 0.1899 0.2214 REMARK 3 4 2.6873 - 2.4416 1.00 7281 366 0.1961 0.2204 REMARK 3 5 2.4416 - 2.2666 1.00 7196 396 0.1993 0.2232 REMARK 3 6 2.2666 - 2.1330 1.00 7180 412 0.2071 0.2399 REMARK 3 7 2.1330 - 2.0261 1.00 7225 358 0.2192 0.2428 REMARK 3 8 2.0261 - 1.9379 1.00 7196 364 0.2268 0.2612 REMARK 3 9 1.9379 - 1.8633 1.00 7158 377 0.2316 0.2529 REMARK 3 10 1.8633 - 1.7990 0.95 6824 331 0.2703 0.2861 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 47.47 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.56500 REMARK 3 B22 (A**2) : -0.56500 REMARK 3 B33 (A**2) : -10.15390 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 : 0.007 3380 REMARK 3 ANGLE : 1.086 4594 REMARK 3 CHIRALITY : 0.075 508 REMARK 3 PLANARITY : 0.004 592 REMARK 3 DIHEDRAL : 14.350 1290 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: NULL REMARK 4 REMARK 4 4AJA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1290051305. 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1AI2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.85 M NH4SO4, 50 MM CITRIC REMARK 280 ACID/NA2HPO4 BUFFER PH 5.8, 0.1 M NACL AND 0.2 M DTT REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 74.78150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.00500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.00500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.17225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.00500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.00500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.39075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.00500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.00500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.17225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.00500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.00500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.39075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 74.78150 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: 10760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.7 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 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 HOH A 2085 O HOH A 2228 1.80 REMARK 500 NZ LYS A 187 O HOH A 2303 1.97 REMARK 500 O HOH A 2064 O HOH A 2419 1.99 REMARK 500 O HOH A 2258 O HOH A 2309 1.99 REMARK 500 OE1 GLU A 215 O HOH A 2325 2.00 REMARK 500 OE2 GLU A 215 O HOH A 2323 2.01 REMARK 500 OE2 GLU A 215 O HOH A 2324 2.06 REMARK 500 O HOH A 2064 O HOH A 2188 2.08 REMARK 500 O HOH A 2218 O HOH A 2219 2.09 REMARK 500 OE1 GLU A 94 O HOH A 2150 2.10 REMARK 500 O HOH A 2217 O HOH A 2452 2.11 REMARK 500 O HOH A 2215 O HOH A 2227 2.12 REMARK 500 O HOH A 2502 O HOH A 2504 2.14 REMARK 500 O HOH A 2486 O HOH A 2496 2.15 REMARK 500 O HOH A 2491 O HOH A 2492 2.15 REMARK 500 OH TYR A 78 OE2 GLU A 87 2.16 REMARK 500 O GLN A 80 O HOH A 2136 2.18 REMARK 500 O HOH A 2079 O HOH A 2489 2.18 REMARK 500 OE1 GLU A 94 O HOH A 2156 2.19 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 O HOH A 2036 O HOH A 2354 5454 2.13 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 ARG A 96 -36.61 74.67 REMARK 500 SER A 113 120.77 -34.65 REMARK 500 GLU A 157 -155.76 -129.96 REMARK 500 ASP A 158 -176.84 69.08 REMARK 500 LYS A 230 59.14 -116.61 REMARK 500 ASP A 259 -124.95 53.10 REMARK 500 ARG A 292 49.21 -140.19 REMARK 500 ASP A 297 -96.75 -137.34 REMARK 500 ALA A 342 59.34 30.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2048 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A2133 DISTANCE = 6.00 ANGSTROMS 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 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 283 OD2 REMARK 620 2 ASP A 307 OD1 86.9 REMARK 620 3 ASP A 311 OD2 67.4 106.9 REMARK 620 4 ICT A 502 O2 137.0 88.4 153.1 REMARK 620 5 ICT A 502 O7 75.4 98.9 132.8 63.1 REMARK 620 6 HOH A2208 O 137.7 80.6 77.9 83.1 146.3 REMARK 620 7 HOH A2411 O 107.4 164.4 74.3 85.1 90.8 84.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TAP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AJ3 RELATED DB: PDB REMARK 900 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE IN COMPLEX WITH REMARK 900 ISOCITRATE, CALCIUM(II) AND NADP - THE PSEUDO-MICHAELIS COMPLEX REMARK 900 RELATED ID: 4AJB RELATED DB: PDB REMARK 900 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE K100M MUTANT IN REMARK 900 COMPLEX WITH ISOCITRATE, CALCIUM(II) AND THIONADP REMARK 900 RELATED ID: 4AJC RELATED DB: PDB REMARK 900 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE K100M MUTANT IN REMARK 900 COMPLEX WITH ALPHA-KETOGLUTARATE, CALCIUM(II ) AND ADENINE REMARK 900 NUCLEOTIDE PHOSPHATE DBREF 4AJA A 1 416 UNP P08200 IDH_ECOLI 1 416 SEQRES 1 A 416 MET GLU SER LYS VAL VAL VAL PRO ALA GLN GLY LYS LYS SEQRES 2 A 416 ILE THR LEU GLN ASN GLY LYS LEU ASN VAL PRO GLU ASN SEQRES 3 A 416 PRO ILE ILE PRO TYR ILE GLU GLY ASP GLY ILE GLY VAL SEQRES 4 A 416 ASP VAL THR PRO ALA MET LEU LYS VAL VAL ASP ALA ALA SEQRES 5 A 416 VAL GLU LYS ALA TYR LYS GLY GLU ARG LYS ILE SER TRP SEQRES 6 A 416 MET GLU ILE TYR THR GLY GLU LYS SER THR GLN VAL TYR SEQRES 7 A 416 GLY GLN ASP VAL TRP LEU PRO ALA GLU THR LEU ASP LEU SEQRES 8 A 416 ILE ARG GLU TYR ARG VAL ALA ILE LYS GLY PRO LEU THR SEQRES 9 A 416 THR PRO VAL GLY GLY GLY ILE ARG SER LEU ASN VAL ALA SEQRES 10 A 416 LEU ARG GLN GLU LEU ASP LEU TYR ILE CYS LEU ARG PRO SEQRES 11 A 416 VAL ARG TYR TYR GLN GLY THR PRO SER PRO VAL LYS HIS SEQRES 12 A 416 PRO GLU LEU THR ASP MET VAL ILE PHE ARG GLU ASN SER SEQRES 13 A 416 GLU ASP ILE TYR ALA GLY ILE GLU TRP LYS ALA ASP SER SEQRES 14 A 416 ALA ASP ALA GLU LYS VAL ILE LYS PHE LEU ARG GLU GLU SEQRES 15 A 416 MET GLY VAL LYS LYS ILE ARG PHE PRO GLU HIS CYS GLY SEQRES 16 A 416 ILE GLY ILE LYS PRO CYS SER GLU GLU GLY THR LYS ARG SEQRES 17 A 416 LEU VAL ARG ALA ALA ILE GLU TYR ALA ILE ALA ASN ASP SEQRES 18 A 416 ARG ASP SER VAL THR LEU VAL HIS LYS GLY ASN ILE MET SEQRES 19 A 416 LYS PHE THR GLU GLY ALA PHE LYS ASP TRP GLY TYR GLN SEQRES 20 A 416 LEU ALA ARG GLU GLU PHE GLY GLY GLU LEU ILE ASP GLY SEQRES 21 A 416 GLY PRO TRP LEU LYS VAL LYS ASN PRO ASN THR GLY LYS SEQRES 22 A 416 GLU ILE VAL ILE LYS ASP VAL ILE ALA ASP ALA PHE LEU SEQRES 23 A 416 GLN GLN ILE LEU LEU ARG PRO ALA GLU TYR ASP VAL ILE SEQRES 24 A 416 ALA CYS MET ASN LEU ASN GLY ASP TYR ILE SER ASP ALA SEQRES 25 A 416 LEU ALA ALA GLN VAL GLY GLY ILE GLY ILE ALA PRO GLY SEQRES 26 A 416 ALA ASN ILE GLY ASP GLU CYS ALA LEU PHE GLU ALA THR SEQRES 27 A 416 HIS GLY THR ALA PRO LYS TYR ALA GLY GLN ASP LYS VAL SEQRES 28 A 416 ASN PRO GLY SER ILE ILE LEU SER ALA GLU MET MET LEU SEQRES 29 A 416 ARG HIS MET GLY TRP THR GLU ALA ALA ASP LEU ILE VAL SEQRES 30 A 416 LYS GLY MET GLU GLY ALA ILE ASN ALA LYS THR VAL THR SEQRES 31 A 416 TYR ASP PHE GLU ARG LEU MET ASP GLY ALA LYS LEU LEU SEQRES 32 A 416 LYS CYS SER GLU PHE GLY ASP ALA ILE ILE GLU ASN MET HET TAP A 501 48 HET ICT A 502 13 HET CA A 503 1 HET SO4 A 504 5 HETNAM TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM ICT ISOCITRIC ACID HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETSYN TAP TATP FORMUL 2 TAP C21 H28 N7 O16 P3 S FORMUL 3 ICT C6 H8 O7 FORMUL 4 CA CA 2+ FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *507(H2 O) HELIX 1 1 ILE A 37 LYS A 58 1 22 HELIX 2 2 GLY A 71 GLY A 79 1 9 HELIX 3 3 PRO A 85 ARG A 96 1 12 HELIX 4 4 SER A 113 LEU A 122 1 10 HELIX 5 5 HIS A 143 LEU A 146 5 4 HELIX 6 6 GLU A 157 GLY A 162 5 6 HELIX 7 7 SER A 169 GLU A 182 1 14 HELIX 8 8 SER A 202 ASN A 220 1 19 HELIX 9 9 THR A 237 GLY A 254 1 18 HELIX 10 10 ALA A 282 ARG A 292 1 11 HELIX 11 11 PRO A 293 TYR A 296 5 4 HELIX 12 12 MET A 302 VAL A 317 1 16 HELIX 13 13 ALA A 342 ALA A 346 5 5 HELIX 14 14 PRO A 353 MET A 367 1 15 HELIX 15 15 TRP A 369 ALA A 386 1 18 HELIX 16 16 THR A 390 ARG A 395 1 6 HELIX 17 17 LYS A 404 ASN A 415 1 12 SHEET 1 AA 2 THR A 15 GLN A 17 0 SHEET 2 AA 2 LYS A 20 ASN A 22 -1 O LYS A 20 N GLN A 17 SHEET 1 AB12 SER A 64 ILE A 68 0 SHEET 2 AB12 ILE A 28 ILE A 32 1 O ILE A 29 N MET A 66 SHEET 3 AB12 VAL A 97 LYS A 100 1 O ILE A 99 N ILE A 32 SHEET 4 AB12 ALA A 333 ALA A 337 1 O ALA A 333 N ALA A 98 SHEET 5 AB12 PRO A 324 ILE A 328 -1 O GLY A 325 N GLU A 336 SHEET 6 AB12 ILE A 126 ARG A 132 -1 O ILE A 126 N ILE A 328 SHEET 7 AB12 ASP A 148 GLU A 154 -1 O MET A 149 N VAL A 131 SHEET 8 AB12 VAL A 298 CYS A 301 1 O ILE A 299 N PHE A 152 SHEET 9 AB12 SER A 224 HIS A 229 1 O SER A 224 N VAL A 298 SHEET 10 AB12 GLU A 274 ILE A 281 1 O VAL A 276 N VAL A 225 SHEET 11 AB12 LEU A 264 LYS A 267 -1 O LEU A 264 N ILE A 277 SHEET 12 AB12 GLU A 256 LEU A 257 -1 O GLU A 256 N LYS A 265 SHEET 1 AC 2 GLU A 164 TRP A 165 0 SHEET 2 AC 2 ILE A 196 GLY A 197 -1 O ILE A 196 N TRP A 165 SHEET 1 AD 2 THR A 388 VAL A 389 0 SHEET 2 AD 2 LYS A 401 LEU A 402 1 O LYS A 401 N VAL A 389 LINK OD2 ASP A 283 CA CA A 503 7555 1555 2.50 LINK OD1 ASP A 307 CA CA A 503 1555 1555 2.36 LINK OD2 ASP A 311 CA CA A 503 1555 1555 2.51 LINK O2 ICT A 502 CA CA A 503 1555 1555 2.45 LINK O7 ICT A 502 CA CA A 503 1555 1555 2.54 LINK CA CA A 503 O HOH A2208 1555 1555 2.64 LINK CA CA A 503 O HOH A2411 1555 1555 2.57 CISPEP 1 GLY A 261 PRO A 262 0 4.61 SITE 1 AC1 30 LYS A 58 LEU A 103 THR A 104 THR A 105 SITE 2 AC1 30 ASN A 115 ILE A 281 HIS A 339 GLY A 340 SITE 3 AC1 30 THR A 341 ALA A 342 TYR A 345 ASN A 352 SITE 4 AC1 30 TYR A 391 ASP A 392 ARG A 395 ICT A 502 SITE 5 AC1 30 HOH A2169 HOH A2424 HOH A2425 HOH A2428 SITE 6 AC1 30 HOH A2429 HOH A2434 HOH A2476 HOH A2499 SITE 7 AC1 30 HOH A2500 HOH A2501 HOH A2502 HOH A2503 SITE 8 AC1 30 HOH A2504 HOH A2505 SITE 1 AC2 15 SER A 113 ASN A 115 ARG A 119 ARG A 129 SITE 2 AC2 15 ARG A 153 TYR A 160 LYS A 230 ASN A 232 SITE 3 AC2 15 ASP A 283 ASP A 307 TAP A 501 CA A 503 SITE 4 AC2 15 HOH A2171 HOH A2423 HOH A2500 SITE 1 AC3 6 ASP A 283 ASP A 307 ASP A 311 ICT A 502 SITE 2 AC3 6 HOH A2208 HOH A2411 SITE 1 AC4 7 VAL A 107 GLY A 108 GLY A 109 GLY A 110 SITE 2 AC4 7 ILE A 111 LYS A 235 HOH A2177 CRYST1 104.010 104.010 149.563 90.00 90.00 90.00 P 43 21 2 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 0.009614 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006686 0.00000