HEADER PROTEIN BINDING 12-MAY-14 4QCJ TITLE CRYSTAL STRUCTURE OF ODHI FROM CORYNEBACTERIUM GLUTAMICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXOGLUTARATE DEHYDROGENASE INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM GLUTAMICUM; SOURCE 3 ORGANISM_TAXID: 196627; SOURCE 4 STRAIN: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025; SOURCE 5 GENE: CG1630, CGL1441, ODHI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FHA-DOMAIN, SIGNAL TRANSDUCTION, ODHA, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.LABAHN,K.RAASCH,L.EGGELING,M.BOCOLA,A.LEITNER,M.BOTT REVDAT 3 28-FEB-24 4QCJ 1 REMARK REVDAT 2 31-DEC-14 4QCJ 1 JRNL REVDAT 1 02-JUL-14 4QCJ 0 JRNL AUTH K.RAASCH,M.BOCOLA,J.LABAHN,A.LEITNER,L.EGGELING,M.BOTT JRNL TITL INTERACTION OF 2-OXOGLUTARATE DEHYDROGENASE ODHA WITH ITS JRNL TITL 2 INHIBITOR ODHI IN CORYNEBACTERIUM GLUTAMICUM: MUTANTS AND A JRNL TITL 3 MODEL. JRNL REF J.BIOTECHNOL. V. 191 99 2014 JRNL REFN ISSN 0168-1656 JRNL PMID 24905147 JRNL DOI 10.1016/J.JBIOTEC.2014.05.023 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 6611 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.670 REMARK 3 FREE R VALUE TEST SET COUNT : 639 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 29.1930 - 3.4191 0.98 1257 133 0.1616 0.2289 REMARK 3 2 3.4191 - 2.7144 0.99 1193 123 0.1797 0.2203 REMARK 3 3 2.7144 - 2.3715 0.99 1179 129 0.1837 0.2634 REMARK 3 4 2.3715 - 2.1547 0.99 1167 129 0.1738 0.2695 REMARK 3 5 2.1547 - 2.0003 1.00 1176 125 0.1832 0.2395 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.240 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 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 : 0.007 791 REMARK 3 ANGLE : 1.057 1072 REMARK 3 CHIRALITY : 0.072 120 REMARK 3 PLANARITY : 0.004 146 REMARK 3 DIHEDRAL : 12.841 294 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 35.0905 11.7625 17.6888 REMARK 3 T TENSOR REMARK 3 T11: 0.0545 T22: 0.0289 REMARK 3 T33: 0.0281 T12: 0.0035 REMARK 3 T13: 0.0489 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 0.1050 L22: 0.0675 REMARK 3 L33: 0.0574 L12: -0.0238 REMARK 3 L13: 0.0238 L23: 0.0027 REMARK 3 S TENSOR REMARK 3 S11: 0.0646 S12: 0.0187 S13: -0.0584 REMARK 3 S21: -0.0109 S22: -0.0593 S23: 0.0067 REMARK 3 S31: 0.0083 S32: -0.0045 S33: 0.0829 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 4QCJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085882. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6634 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 51.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 18.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG 3350, 0.2 M SODIUM MALONATE, REMARK 280 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 25.51300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.61450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.51300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.61450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A 287 LIES ON A SPECIAL POSITION. 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 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 ASN A 4 REMARK 465 ASN A 5 REMARK 465 GLY A 6 REMARK 465 THR A 7 REMARK 465 PRO A 8 REMARK 465 GLU A 9 REMARK 465 PRO A 10 REMARK 465 GLN A 11 REMARK 465 VAL A 12 REMARK 465 GLU A 13 REMARK 465 THR A 14 REMARK 465 THR A 15 REMARK 465 SER A 16 REMARK 465 VAL A 17 REMARK 465 PHE A 18 REMARK 465 ARG A 19 REMARK 465 ALA A 20 REMARK 465 ASP A 21 REMARK 465 LEU A 22 REMARK 465 LEU A 23 REMARK 465 LYS A 24 REMARK 465 GLU A 25 REMARK 465 MET A 26 REMARK 465 GLU A 27 REMARK 465 SER A 28 REMARK 465 SER A 29 REMARK 465 THR A 30 REMARK 465 GLY A 31 REMARK 465 THR A 32 REMARK 465 ALA A 33 REMARK 465 PRO A 34 REMARK 465 ALA A 35 REMARK 465 SER A 36 REMARK 465 THR A 37 REMARK 465 GLY A 38 REMARK 465 ALA A 39 REMARK 465 GLU A 40 REMARK 465 ASN A 41 REMARK 465 GLU A 143 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 313 O HOH A 332 2.18 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 ASP A 64 37.32 -146.16 REMARK 500 ARG A 114 -3.70 79.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 4QCJ A 1 143 UNP Q8NQJ3 ODHI_CORGL 1 143 SEQRES 1 A 143 MET SER ASP ASN ASN GLY THR PRO GLU PRO GLN VAL GLU SEQRES 2 A 143 THR THR SER VAL PHE ARG ALA ASP LEU LEU LYS GLU MET SEQRES 3 A 143 GLU SER SER THR GLY THR ALA PRO ALA SER THR GLY ALA SEQRES 4 A 143 GLU ASN LEU PRO ALA GLY SER ALA LEU LEU VAL VAL LYS SEQRES 5 A 143 ARG GLY PRO ASN ALA GLY ALA ARG PHE LEU LEU ASP GLN SEQRES 6 A 143 PRO THR THR THR ALA GLY ARG HIS PRO GLU SER ASP ILE SEQRES 7 A 143 PHE LEU ASP ASP VAL THR VAL SER ARG ARG HIS ALA GLU SEQRES 8 A 143 PHE ARG ILE ASN GLU GLY GLU PHE GLU VAL VAL ASP VAL SEQRES 9 A 143 GLY SER LEU ASN GLY THR TYR VAL ASN ARG GLU PRO ARG SEQRES 10 A 143 ASN ALA GLN VAL MET GLN THR GLY ASP GLU ILE GLN ILE SEQRES 11 A 143 GLY LYS PHE ARG LEU VAL PHE LEU ALA GLY PRO ALA GLU FORMUL 2 HOH *135(H2 O) SHEET 1 A 6 ARG A 60 LEU A 63 0 SHEET 2 A 6 ALA A 47 ARG A 53 -1 N ALA A 47 O LEU A 63 SHEET 3 A 6 PHE A 133 ALA A 139 -1 O ARG A 134 N LYS A 52 SHEET 4 A 6 GLU A 127 ILE A 130 -1 N ILE A 128 O LEU A 135 SHEET 5 A 6 THR A 110 VAL A 112 -1 N TYR A 111 O GLN A 129 SHEET 6 A 6 GLU A 115 PRO A 116 -1 O GLU A 115 N VAL A 112 SHEET 1 B 5 ILE A 78 PHE A 79 0 SHEET 2 B 5 THR A 67 GLY A 71 1 N THR A 69 O ILE A 78 SHEET 3 B 5 ALA A 90 ILE A 94 -1 O PHE A 92 N THR A 68 SHEET 4 B 5 PHE A 99 ASP A 103 -1 O GLU A 100 N ARG A 93 SHEET 5 B 5 ALA A 119 VAL A 121 -1 O GLN A 120 N VAL A 101 CISPEP 1 ASN A 95 GLU A 96 0 -2.28 CRYST1 51.026 51.229 35.520 90.00 90.00 90.00 P 21 21 2 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 0.019598 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028153 0.00000