HEADER OXIDOREDUCTASE(NAD(A)-CHOH(D)) 15-JUN-93 1IKB OBSLTE 15-OCT-97 1IKB 1AI2 TITLE THE STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ISOCITRATE, TITLE 2 NADP, AND CALCIUM AT 2.5 ANGSTROMS RESOLUTION: A PSEUDO- TITLE 3 MICHAELIS TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS OXIDOREDUCTASE(NAD(A)-CHOH(D)) EXPDTA X-RAY DIFFRACTION AUTHOR B.L.STODDARD,D.E.KOSHLAND JUNIOR REVDAT 1 31-JUL-94 1IKB 0 JRNL AUTH B.L.STODDARD,A.DEAN,D.E.KOSHLAND JUNIOR JRNL TITL THE STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH JRNL TITL 2 ISOCITRATE, NADP, AND CALCIUM AT 2.5 ANGSTROMS JRNL TITL 3 RESOLUTION: A PSEUDO-MICHAELIS TERNARY COMPLEX JRNL REF BIOCHEMISTRY V. 32 9310 1993 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.L.STODDARD,D.E.KOSHLAND JUNIOR REMARK 1 TITL STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH REMARK 1 TITL 2 ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: REMARK 1 TITL 3 CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION REMARK 1 TITL 4 OF ISOCITRATE REMARK 1 REF BIOCHEMISTRY V. 32 9317 1993 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 1IKB REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 24628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 3.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IKB COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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,1/2+Z REMARK 290 3555 1/2-Y,1/2+X,3/4+Z REMARK 290 4555 1/2+Y,1/2-X,1/4+Z REMARK 290 5555 1/2-X,1/2+Y,3/4-Z REMARK 290 6555 1/2+X,1/2-Y,1/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,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 75.15000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.55000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.72500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.55000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.55000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.57500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.55000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.55000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.72500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.55000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.55000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.57500 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 75.15000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 1 REMARK 465 GLU 2 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 REMARK 500 CG2 VAL 116 O6 ICT 1 1.49 REMARK 500 CB ASN 115 NO7 NAP 2 2.06 REMARK 500 OD1 ASN 115 OE2 GLU 336 2.06 REMARK 500 NH2 ARG 119 O1 ICT 1 2.12 REMARK 500 O3 ICT 1 NC2 NAP 2 2.14 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP 307 CA ASP 307 CB 0.131 REMARK 500 ASP 307 CB ASP 307 CG 0.173 REMARK 500 ASP 307 CG ASP 307 OD1 0.162 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 M RES CSSEQI PSI PHI REMARK 500 LYS 4 -44.23 51.36 REMARK 500 GLU 25 -64.20 44.25 REMARK 500 ASP 168 -36.59 76.92 REMARK 500 THR 237 -73.73 33.69 REMARK 500 ASP 259 -68.29 46.11 SEQRES 1 416 MET GLU SER LYS VAL VAL VAL PRO ALA GLN GLY LYS LYS SEQRES 2 416 ILE THR LEU GLN ASN GLY LYS LEU ASN VAL PRO GLU ASN SEQRES 3 416 PRO ILE ILE PRO TYR ILE GLU GLY ASP GLY ILE GLY VAL SEQRES 4 416 ASP VAL THR PRO ALA MET LEU LYS VAL VAL ASP ALA ALA SEQRES 5 416 VAL GLU LYS ALA TYR LYS GLY GLU ARG LYS ILE SER TRP SEQRES 6 416 MET GLU ILE TYR THR GLY GLU LYS SER THR GLN VAL TYR SEQRES 7 416 GLY GLN ASP VAL TRP LEU PRO ALA GLU THR LEU ASP LEU SEQRES 8 416 ILE ARG GLU TYR ARG VAL ALA ILE LYS GLY PRO LEU THR SEQRES 9 416 THR PRO VAL GLY GLY GLY ILE ARG SER LEU ASN VAL ALA SEQRES 10 416 LEU ARG GLN GLU LEU ASP LEU TYR ILE CYS LEU ARG PRO SEQRES 11 416 VAL ARG TYR TYR GLN GLY THR PRO SER PRO VAL LYS HIS SEQRES 12 416 PRO GLU LEU THR ASP MET VAL ILE PHE ARG GLU ASN SER SEQRES 13 416 GLU ASP ILE TYR ALA GLY ILE GLU TRP LYS ALA ASP SER SEQRES 14 416 ALA ASP ALA GLU LYS VAL ILE LYS PHE LEU ARG GLU GLU SEQRES 15 416 MET GLY VAL LYS LYS ILE ARG PHE PRO GLU HIS CYS GLY SEQRES 16 416 ILE GLY ILE LYS PRO CYS SER GLU GLU GLY THR LYS ARG SEQRES 17 416 LEU VAL ARG ALA ALA ILE GLU TYR ALA ILE ALA ASN ASP SEQRES 18 416 ARG ASP SER VAL THR LEU VAL HIS LYS GLY ASN ILE MET SEQRES 19 416 LYS PHE THR GLU GLY ALA PHE LYS ASP TRP GLY TYR GLN SEQRES 20 416 LEU ALA ARG GLU GLU PHE GLY GLY GLU LEU ILE ASP GLY SEQRES 21 416 GLY PRO TRP LEU LYS VAL LYS ASN PRO ASN THR GLY LYS SEQRES 22 416 GLU ILE VAL ILE LYS ASP VAL ILE ALA ASP ALA PHE LEU SEQRES 23 416 GLN GLN ILE LEU LEU ARG PRO ALA GLU TYR ASP VAL ILE SEQRES 24 416 ALA CYS MET ASN LEU ASN GLY ASP TYR ILE SER ASP ALA SEQRES 25 416 LEU ALA ALA GLN VAL GLY GLY ILE GLY ILE ALA PRO GLY SEQRES 26 416 ALA ASN ILE GLY ASP GLU CYS ALA LEU PHE GLU ALA THR SEQRES 27 416 HIS GLY THR ALA PRO LYS TYR ALA GLY GLN ASP LYS VAL SEQRES 28 416 ASN PRO GLY SER ILE ILE LEU SER ALA GLU MET MET LEU SEQRES 29 416 ARG HIS MET GLY TRP THR GLU ALA ALA ASP LEU ILE VAL SEQRES 30 416 LYS GLY MET GLU GLY ALA ILE ASN ALA LYS THR VAL THR SEQRES 31 416 TYR ASP PHE GLU ARG LEU MET ASP GLY ALA LYS LEU LEU SEQRES 32 416 LYS CYS SER GLU PHE GLY ASP ALA ILE ILE GLU ASN MET FTNOTE 1 CIS PROLINE - PRO 262 HET CA 2 1 HET ICT 1 13 HET NAP 2 48 HETNAM CA CALCIUM ION HETNAM ICT ISOCITRIC ACID HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 CA CA 2+ FORMUL 3 ICT C6 H8 O7 FORMUL 4 NAP C21 H28 N7 O17 P3 FORMUL 5 HOH *2(H2 O1) HELIX 1 HA ILE 37 LYS 58 1 22 HELIX 2 HB THR 70 TYR 78 1 9 HELIX 3 HC PRO 85 TYR 95 1 11 HELIX 4 HD SER 113 LEU 124 1 12 HELIX 5 HE ASP 168 MET 183 1 16 HELIX 6 HF GLU 203 ARG 222 1 20 HELIX 7 HG LYS 235 PHE 253 1 19 HELIX 8 HH ILE 281 LEU 291 1 11 HELIX 9 HI ASN 303 VAL 317 1 15 HELIX 10 HJ PRO 353 MET 367 1 15 HELIX 11 HK TRP 369 THR 388 1 20 HELIX 12 HL THR 390 MET 397 1 8 HELIX 13 HM LYS 404 ASN 415 1 12 SHEET 1 S112 ARG 61 ILE 68 0 SHEET 2 S112 GLU 25 ILE 32 1 SHEET 3 S112 ARG 96 LYS 100 1 SHEET 4 S112 ALA 333 GLU 336 1 SHEET 5 S112 GLY 325 ILE 328 -1 SHEET 6 S112 TYR 125 ARG 132 -1 SHEET 7 S112 THR 147 ARG 153 -1 SHEET 8 S112 ASP 297 MET 302 1 SHEET 9 S112 SER 224 HIS 229 1 SHEET 10 S112 LYS 273 VAL 280 1 SHEET 11 S112 LEU 264 LYS 267 -1 SHEET 12 S112 GLY 254 GLU 256 -1 SHEET 1 S2 2 ILE 163 ALA 167 0 SHEET 2 S2 2 HIS 193 SER 202 -1 CISPEP 1 GLY 261 PRO 262 0 -22.38 CRYST1 105.100 105.100 150.300 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 0.009515 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006653 0.00000