HEADER OXIDOREDUCTASE 30-MAR-12 4AOV TITLE DPIDH-NADP. THE COMPLEX STRUCTURES OF ISOCITRATE DEHYDROGENASE FROM TITLE 2 CLOSTRIDIUM THERMOCELLUM AND DESULFOTALEA PSYCHROPHILA, SUPPORT A NEW TITLE 3 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: DESULFOTALEA PSYCHROPHILA; SOURCE 3 ORGANISM_TAXID: 84980; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: EB106 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 5 08-MAY-24 4AOV 1 REMARK LINK REVDAT 4 08-MAY-19 4AOV 1 REMARK REVDAT 3 22-MAY-13 4AOV 1 JRNL REVDAT 2 20-MAR-13 4AOV 1 JRNL REVDAT 1 11-JUL-12 4AOV 0 JRNL AUTH H.-K.S.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. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0021 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 29252 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1563 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1830 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3180 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 227 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.52000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.166 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.883 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3360 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4558 ; 1.406 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 411 ; 6.189 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;36.956 ;24.503 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 580 ;14.282 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.199 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 500 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2528 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1555 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2327 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 238 ; 0.149 ; 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): 126 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 40 ; 0.161 ; 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): 2102 ; 0.700 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3279 ; 1.090 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1468 ; 1.715 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1279 ; 2.495 ; 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 4AOV 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_1290051917. 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 : ESRF REMARK 200 BEAMLINE : BM1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8536 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30844 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP METHOD. RESERVOIR REMARK 280 SOLUTIONS WITH 100 MM TRIS/HCL BUFFER AT PH 7.4, 1.7-1.9 M REMARK 280 AMMONIUM SULFATE, 2% PEG 400 AND 60 MM MAGNESIUM SULFATE. REMARK 280 PROTEIN SOLUTION: 20 MG/ML DPIDH, 10 MM NADP AND 10 MM DL- REMARK 280 ISOCITRATE., VAPOR DIFFUSION, HANGING DROP 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 30.82000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.45500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.82000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 49.45500 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: 12100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.8 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 44.32129 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 69.77273 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2128 LIES ON A SPECIAL POSITION. 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 92 CD CE NZ REMARK 470 LYS A 114 CD CE NZ REMARK 470 LYS A 117 CD CE NZ REMARK 470 LYS A 158 CG REMARK 470 LYS A 161 CE NZ REMARK 470 LYS A 201 CD CE NZ REMARK 470 GLU A 259 OE1 REMARK 470 LYS A 395 CE NZ REMARK 470 GLN A 399 CD OE1 NE2 REMARK 470 ASN A 401 CA 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 2169 O HOH A 2170 2.02 REMARK 500 OE1 GLU A 146 O HOH A 2106 2.19 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 16 -133.57 47.47 REMARK 500 ASN A 78 -167.15 -103.38 REMARK 500 ASP A 103 160.99 62.63 REMARK 500 ASP A 136 -140.31 55.30 REMARK 500 LYS A 209 66.73 -112.42 REMARK 500 TYR A 216 -70.18 -99.36 REMARK 500 SER A 322 51.87 -116.59 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 MG A1405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 249 OD2 REMARK 620 2 ASP A 272 OD1 90.6 REMARK 620 3 ICT A1404 O1 168.6 90.4 REMARK 620 4 ICT A1404 O7 91.5 91.7 77.1 REMARK 620 5 HOH A2067 O 102.5 86.8 88.9 165.9 REMARK 620 6 HOH A2177 O 91.5 175.1 88.4 92.6 88.4 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 NAP A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT A 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2UXQ RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE FROM THE PSYCHROPHILIC BACTERIUM REMARK 900 DESULFOTALEA PSYCHROPHILA: BIOCHEMICAL PROPERTIES AND CRYSTAL REMARK 900 STRUCTURE ANALYSIS REMARK 900 RELATED ID: 2UXR RELATED DB: PDB REMARK 900 COMPLEX WITH ISOCITRATE AND THE PROTEIN ISOCITRATE DEHYDROGENASE REMARK 900 FROM THE PSYCHROPHILIC BACTERIUM DESULFOTALEA PSYCHROPHILA REMARK 900 RELATED ID: 4AOU RELATED DB: PDB REMARK 900 CTIDH BOUND TO NADP. THE COMPLEX STRUCTURES OF ISOCITRATE REMARK 900 DEHYDROGENASE FROM CLOSTRIDIUM THERMOCELLUM AND DESULFOTALEA REMARK 900 PSYCHROPHILA, SUPPORT A NEW ACTIVE SITE LOCKING MECHANISM DBREF 4AOV A 1 402 UNP Q6AQ66 Q6AQ66_DESPS 1 402 SEQRES 1 A 402 MET LYS ILE GLN MET LYS THR PRO LEU VAL GLU LEU ASP SEQRES 2 A 402 GLY ASP GLU MET THR ARG VAL LEU TRP PRO LEU ILE LYS SEQRES 3 A 402 ASP LYS LEU LEU LEU PRO PHE ILE ASP LEU GLN THR GLU SEQRES 4 A 402 TYR TYR ASP LEU GLY ILE GLU GLU ARG ASP ARG THR ASN SEQRES 5 A 402 ASP GLN ILE THR ILE ASP ALA ALA GLU ALA ILE LYS LYS SEQRES 6 A 402 TYR GLY VAL GLY VAL LYS ASN ALA THR ILE THR PRO ASN SEQRES 7 A 402 GLN ASP ARG VAL GLU GLU TYR GLY LEU LYS GLU GLN TRP SEQRES 8 A 402 LYS SER PRO ASN ALA THR VAL ARG ALA MET LEU ASP GLY SEQRES 9 A 402 THR VAL PHE ARG LYS PRO ILE MET VAL LYS ASN ILE LYS SEQRES 10 A 402 PRO SER VAL ARG SER TRP GLN LYS PRO ILE VAL VAL GLY SEQRES 11 A 402 ARG HIS ALA TYR GLY ASP PHE TYR LYS ASN ALA GLU ILE SEQRES 12 A 402 PHE ALA GLU ALA GLY GLY LYS LEU GLU ILE VAL VAL THR SEQRES 13 A 402 ASP LYS ASN GLY LYS GLU THR ARG GLN THR ILE MET GLU SEQRES 14 A 402 VAL ASP GLU PRO ALA ILE VAL GLN GLY ILE HIS ASN THR SEQRES 15 A 402 VAL ALA SER ILE GLY HIS PHE ALA ARG ALA CYS PHE GLU SEQRES 16 A 402 TYR SER LEU ASP GLN LYS ILE ASP CYS TRP PHE ALA THR SEQRES 17 A 402 LYS ASP THR ILE SER LYS GLN TYR ASP GLN ARG PHE LYS SEQRES 18 A 402 ILE ILE PHE GLU GLU ILE PHE ALA GLN GLU TYR LYS GLU SEQRES 19 A 402 LYS PHE ALA ALA ALA GLY ILE GLU TYR PHE TYR THR LEU SEQRES 20 A 402 ILE ASP ASP VAL VAL ALA ARG MET MET LYS THR GLU GLY SEQRES 21 A 402 GLY MET LEU TRP ALA CYS LYS ASN TYR ASP GLY ASP VAL SEQRES 22 A 402 MET SER ASP MET VAL ALA SER ALA PHE GLY SER LEU ALA SEQRES 23 A 402 MET MET SER SER VAL LEU VAL SER PRO TYR GLY TYR PHE SEQRES 24 A 402 GLU TYR GLU ALA ALA HIS GLY THR VAL GLN ARG HIS TYR SEQRES 25 A 402 TYR GLN HIS LEU LYS GLY GLU ARG THR SER THR ASN PRO SEQRES 26 A 402 VAL ALA LEU ILE TYR ALA TRP THR GLY ALA LEU ARG LYS SEQRES 27 A 402 ARG GLY GLU LEU ASP GLY THR PRO ASP LEU CYS ALA PHE SEQRES 28 A 402 CYS ASP SER LEU GLU ALA ILE THR ILE GLU CYS ILE GLU SEQRES 29 A 402 SER GLY TYR MET THR GLY ASP LEU ALA ARG ILE CYS GLU SEQRES 30 A 402 PRO ALA ALA ILE LYS VAL LEU ASP SER ILE GLU PHE ILE SEQRES 31 A 402 ASP GLU LEU GLY LYS ARG LEU GLN GLN LEU ASN LYS HET NAP A1403 48 HET ICT A1404 13 HET MG A1405 1 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM ICT ISOCITRIC ACID HETNAM MG MAGNESIUM ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 ICT C6 H8 O7 FORMUL 4 MG MG 2+ FORMUL 5 HOH *227(H2 O) HELIX 1 1 ASP A 15 LEU A 30 1 16 HELIX 2 2 GLY A 44 THR A 51 1 8 HELIX 3 3 ASP A 53 GLY A 67 1 15 HELIX 4 4 ASN A 78 GLY A 86 1 9 HELIX 5 5 SER A 93 ASP A 103 1 11 HELIX 6 6 THR A 182 LYS A 201 1 20 HELIX 7 7 TYR A 216 TYR A 232 1 17 HELIX 8 8 TYR A 232 ALA A 239 1 8 HELIX 9 9 ILE A 248 THR A 258 1 11 HELIX 10 10 LYS A 267 GLY A 283 1 17 HELIX 11 11 VAL A 308 LYS A 317 1 10 HELIX 12 12 PRO A 325 GLY A 344 1 20 HELIX 13 13 THR A 345 GLY A 366 1 22 HELIX 14 14 THR A 369 ARG A 374 1 6 HELIX 15 15 ASP A 385 ASN A 401 1 17 SHEET 1 AA10 THR A 38 ASP A 42 0 SHEET 2 AA10 LEU A 9 ASP A 13 1 O LEU A 9 N GLU A 39 SHEET 3 AA10 VAL A 68 LYS A 71 1 O VAL A 68 N VAL A 10 SHEET 4 AA10 PHE A 299 ALA A 303 1 O PHE A 299 N GLY A 69 SHEET 5 AA10 MET A 288 VAL A 293 -1 O SER A 290 N GLU A 302 SHEET 6 AA10 THR A 105 PRO A 110 -1 O THR A 105 N VAL A 293 SHEET 7 AA10 VAL A 128 HIS A 132 -1 O VAL A 129 N ARG A 108 SHEET 8 AA10 MET A 262 CYS A 266 1 O MET A 262 N VAL A 128 SHEET 9 AA10 ASP A 203 THR A 208 1 O ASP A 203 N LEU A 263 SHEET 10 AA10 TYR A 243 LEU A 247 1 O PHE A 244 N PHE A 206 SHEET 1 AB 2 ASP A 136 ALA A 145 0 SHEET 2 AB 2 ALA A 174 HIS A 180 -1 O ALA A 174 N ALA A 145 SHEET 1 AC 2 GLY A 149 THR A 156 0 SHEET 2 AC 2 GLU A 162 VAL A 170 -1 O THR A 163 N VAL A 155 SHEET 1 AD 2 TYR A 367 MET A 368 0 SHEET 2 AD 2 LYS A 382 VAL A 383 1 O LYS A 382 N MET A 368 LINK OD2 ASP A 249 MG MG A1405 2656 1555 2.04 LINK OD1 ASP A 272 MG MG A1405 1555 1555 2.05 LINK O1 ICT A1404 MG MG A1405 1555 1555 2.14 LINK O7 ICT A1404 MG MG A1405 1555 1555 2.04 LINK MG MG A1405 O HOH A2067 1555 1555 2.04 LINK MG MG A1405 O HOH A2177 1555 1555 2.04 CISPEP 1 GLU A 377 PRO A 378 0 3.22 SITE 1 AC1 34 ALA A 73 THR A 74 THR A 76 ARG A 81 SITE 2 AC1 34 ASN A 95 ASP A 250 ARG A 254 LEU A 285 SITE 3 AC1 34 ALA A 286 HIS A 305 GLY A 306 THR A 307 SITE 4 AC1 34 VAL A 308 ARG A 310 HIS A 311 THR A 323 SITE 5 AC1 34 ASN A 324 ICT A1404 HOH A2042 HOH A2045 SITE 6 AC1 34 HOH A2115 HOH A2141 HOH A2143 HOH A2163 SITE 7 AC1 34 HOH A2164 HOH A2165 HOH A2166 HOH A2178 SITE 8 AC1 34 HOH A2190 HOH A2192 HOH A2199 HOH A2225 SITE 9 AC1 34 HOH A2226 HOH A2227 SITE 1 AC2 18 THR A 76 SER A 93 ASN A 95 ARG A 99 SITE 2 AC2 18 ARG A 108 ARG A 131 TYR A 138 LYS A 209 SITE 3 AC2 18 ILE A 212 ASP A 249 ASP A 272 ALA A 304 SITE 4 AC2 18 NAP A1403 MG A1405 HOH A2067 HOH A2141 SITE 5 AC2 18 HOH A2143 HOH A2177 SITE 1 AC3 5 ASP A 249 ASP A 272 ICT A1404 HOH A2067 SITE 2 AC3 5 HOH A2177 CRYST1 61.640 98.910 71.890 90.00 103.94 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016223 0.000000 0.004027 0.00000 SCALE2 0.000000 0.010110 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014332 0.00000