HEADER LYASE 16-SEP-04 1XG4 TITLE CRYSTAL STRUCTURE OF THE C123S 2-METHYLISOCITRATE LYASE MUTANT FROM TITLE 2 ESCHERICHIA COLI IN COMPLEX WITH THE INHIBITOR ISOCITRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE METHYLISOCITRATE LYASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: 2-METHYLISOCITRATE LYASE; COMPND 5 EC: 4.1.3.30; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: PRPB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3C KEYWDS 2-METHYLISOCITRATE LYASE-INHIBITOR COMPLEX, ISOCITRATE, ISOCITRATE KEYWDS 2 LYASE SUPERFAMILY, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LIU,Z.LU,Y.HAN,E.MELAMUD,D.DUNAWAY-MARIANO,O.HERZBERG REVDAT 4 23-AUG-23 1XG4 1 REMARK REVDAT 3 20-OCT-21 1XG4 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1XG4 1 VERSN REVDAT 1 01-MAR-05 1XG4 0 JRNL AUTH S.LIU,Z.LU,Y.HAN,E.MELAMUD,D.DUNAWAY-MARIANO,O.HERZBERG JRNL TITL CRYSTAL STRUCTURES OF 2-METHYLISOCITRATE LYASE IN COMPLEX JRNL TITL 2 WITH PRODUCT AND WITH ISOCITRATE INHIBITOR PROVIDE INSIGHT JRNL TITL 3 INTO LYASE SUBSTRATE SPECIFICITY, CATALYSIS AND EVOLUTION JRNL REF BIOCHEMISTRY V. 44 2949 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15723538 JRNL DOI 10.1021/BI0479712 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.9 REMARK 3 NUMBER OF REFLECTIONS : 138747 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 SET) : 0.181 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 4929 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 : 8694 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 982 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) : 2.72900 REMARK 3 B22 (A**2) : -5.95800 REMARK 3 B33 (A**2) : 3.22900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.25100 REMARK 3 B23 (A**2) : 0.00000 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : ITM_XPLOR_PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XG4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92139 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 161348 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 47.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 4.160 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 22.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22700 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1OQF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG3350, 0.1M (NH)2SO4, 0.1M MES REMARK 280 (PH6.0), 5MM MG(II), 5MM ISOCITRATE ACID, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298.0K 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 79.53050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.28050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 79.53050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.28050 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 300 REMARK: ONE ASYMMETRIC UNIT HAS 4 MOLECULES, WHICH FORM BIOLOGICAL REMARK 300 ASSEMBLE OF ENZYME. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 LEU A 289 REMARK 465 PHE A 290 REMARK 465 ALA A 291 REMARK 465 ARG A 292 REMARK 465 SER A 293 REMARK 465 GLN A 294 REMARK 465 VAL A 295 REMARK 465 LYS A 296 REMARK 465 SER B 2 REMARK 465 LEU B 289 REMARK 465 PHE B 290 REMARK 465 ALA B 291 REMARK 465 ARG B 292 REMARK 465 SER B 293 REMARK 465 GLN B 294 REMARK 465 VAL B 295 REMARK 465 LYS B 296 REMARK 465 SER C 2 REMARK 465 PHE C 290 REMARK 465 ALA C 291 REMARK 465 ARG C 292 REMARK 465 SER C 293 REMARK 465 GLN C 294 REMARK 465 VAL C 295 REMARK 465 LYS C 296 REMARK 465 SER D 2 REMARK 465 LEU D 286 REMARK 465 ASP D 287 REMARK 465 ASN D 288 REMARK 465 LEU D 289 REMARK 465 PHE D 290 REMARK 465 ALA D 291 REMARK 465 ARG D 292 REMARK 465 SER D 293 REMARK 465 GLN D 294 REMARK 465 VAL D 295 REMARK 465 LYS D 296 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 284 CD GLU A 284 OE2 0.079 REMARK 500 GLU B 284 CD GLU B 284 OE2 0.068 REMARK 500 GLU C 284 CD GLU C 284 OE2 0.078 REMARK 500 GLU D 284 CD GLU D 284 OE2 0.079 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 87 -118.19 44.96 REMARK 500 ASP B 87 -119.36 46.64 REMARK 500 ASP C 87 -116.01 44.23 REMARK 500 ASN C 288 46.73 -100.43 REMARK 500 ASP D 87 -119.02 44.83 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 A1101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 85 OD2 REMARK 620 2 ICT A1105 O7 100.2 REMARK 620 3 ICT A1105 O2 90.4 65.5 REMARK 620 4 HOH A1360 O 169.7 82.3 99.6 REMARK 620 5 HOH A1361 O 89.7 164.4 102.8 90.0 REMARK 620 6 HOH A1362 O 76.0 95.0 154.1 94.0 99.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 85 OD2 REMARK 620 2 ICT B1205 O2 97.5 REMARK 620 3 ICT B1205 O7 102.9 66.2 REMARK 620 4 HOH B1465 O 166.3 96.2 82.3 REMARK 620 5 HOH B1466 O 92.4 107.8 164.1 83.8 REMARK 620 6 HOH B1467 O 78.2 157.9 93.4 88.9 94.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D1401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 85 OD2 REMARK 620 2 ICT D1405 O2 94.2 REMARK 620 3 ICT D1405 O7 102.0 66.7 REMARK 620 4 HOH D1633 O 170.2 95.0 85.0 REMARK 620 5 HOH D1634 O 91.7 101.8 162.5 82.9 REMARK 620 6 HOH D1635 O 78.3 159.0 95.4 94.3 98.0 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 MG A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT A 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT B 1205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT D 1405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XG3 RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH THE REACTION PRODUCT, MG(II)-PYRUVATE REMARK 900 AND SUCCINATE REMARK 900 RELATED ID: 1OQF RELATED DB: PDB REMARK 900 NATIVE PRPB APO STRUCTURE DBREF 1XG4 A 2 296 UNP P77541 PRPB_ECOLI 1 295 DBREF 1XG4 B 2 296 UNP P77541 PRPB_ECOLI 1 295 DBREF 1XG4 C 2 296 UNP P77541 PRPB_ECOLI 1 295 DBREF 1XG4 D 2 296 UNP P77541 PRPB_ECOLI 1 295 SEQADV 1XG4 SER A 123 UNP P77541 CYS 122 ENGINEERED MUTATION SEQADV 1XG4 SER B 123 UNP P77541 CYS 122 ENGINEERED MUTATION SEQADV 1XG4 SER C 123 UNP P77541 CYS 122 ENGINEERED MUTATION SEQADV 1XG4 SER D 123 UNP P77541 CYS 122 ENGINEERED MUTATION SEQRES 1 A 295 SER LEU HIS SER PRO GLY LYS ALA PHE ARG ALA ALA LEU SEQRES 2 A 295 THR LYS GLU ASN PRO LEU GLN ILE VAL GLY THR ILE ASN SEQRES 3 A 295 ALA ASN HIS ALA LEU LEU ALA GLN ARG ALA GLY TYR GLN SEQRES 4 A 295 ALA ILE TYR LEU SER GLY GLY GLY VAL ALA ALA GLY SER SEQRES 5 A 295 LEU GLY LEU PRO ASP LEU GLY ILE SER THR LEU ASP ASP SEQRES 6 A 295 VAL LEU THR ASP ILE ARG ARG ILE THR ASP VAL CYS SER SEQRES 7 A 295 LEU PRO LEU LEU VAL ASP ALA ASP ILE GLY PHE GLY SER SEQRES 8 A 295 SER ALA PHE ASN VAL ALA ARG THR VAL LYS SER MET ILE SEQRES 9 A 295 LYS ALA GLY ALA ALA GLY LEU HIS ILE GLU ASP GLN VAL SEQRES 10 A 295 GLY ALA LYS ARG SER GLY HIS ARG PRO ASN LYS ALA ILE SEQRES 11 A 295 VAL SER LYS GLU GLU MET VAL ASP ARG ILE ARG ALA ALA SEQRES 12 A 295 VAL ASP ALA LYS THR ASP PRO ASP PHE VAL ILE MET ALA SEQRES 13 A 295 ARG THR ASP ALA LEU ALA VAL GLU GLY LEU ASP ALA ALA SEQRES 14 A 295 ILE GLU ARG ALA GLN ALA TYR VAL GLU ALA GLY ALA GLU SEQRES 15 A 295 MET LEU PHE PRO GLU ALA ILE THR GLU LEU ALA MET TYR SEQRES 16 A 295 ARG GLN PHE ALA ASP ALA VAL GLN VAL PRO ILE LEU ALA SEQRES 17 A 295 ASN ILE THR GLU PHE GLY ALA THR PRO LEU PHE THR THR SEQRES 18 A 295 ASP GLU LEU ARG SER ALA HIS VAL ALA MET ALA LEU TYR SEQRES 19 A 295 PRO LEU SER ALA PHE ARG ALA MET ASN ARG ALA ALA GLU SEQRES 20 A 295 HIS VAL TYR ASN VAL LEU ARG GLN GLU GLY THR GLN LYS SEQRES 21 A 295 SER VAL ILE ASP THR MET GLN THR ARG ASN GLU LEU TYR SEQRES 22 A 295 GLU SER ILE ASN TYR TYR GLN TYR GLU GLU LYS LEU ASP SEQRES 23 A 295 ASN LEU PHE ALA ARG SER GLN VAL LYS SEQRES 1 B 295 SER LEU HIS SER PRO GLY LYS ALA PHE ARG ALA ALA LEU SEQRES 2 B 295 THR LYS GLU ASN PRO LEU GLN ILE VAL GLY THR ILE ASN SEQRES 3 B 295 ALA ASN HIS ALA LEU LEU ALA GLN ARG ALA GLY TYR GLN SEQRES 4 B 295 ALA ILE TYR LEU SER GLY GLY GLY VAL ALA ALA GLY SER SEQRES 5 B 295 LEU GLY LEU PRO ASP LEU GLY ILE SER THR LEU ASP ASP SEQRES 6 B 295 VAL LEU THR ASP ILE ARG ARG ILE THR ASP VAL CYS SER SEQRES 7 B 295 LEU PRO LEU LEU VAL ASP ALA ASP ILE GLY PHE GLY SER SEQRES 8 B 295 SER ALA PHE ASN VAL ALA ARG THR VAL LYS SER MET ILE SEQRES 9 B 295 LYS ALA GLY ALA ALA GLY LEU HIS ILE GLU ASP GLN VAL SEQRES 10 B 295 GLY ALA LYS ARG SER GLY HIS ARG PRO ASN LYS ALA ILE SEQRES 11 B 295 VAL SER LYS GLU GLU MET VAL ASP ARG ILE ARG ALA ALA SEQRES 12 B 295 VAL ASP ALA LYS THR ASP PRO ASP PHE VAL ILE MET ALA SEQRES 13 B 295 ARG THR ASP ALA LEU ALA VAL GLU GLY LEU ASP ALA ALA SEQRES 14 B 295 ILE GLU ARG ALA GLN ALA TYR VAL GLU ALA GLY ALA GLU SEQRES 15 B 295 MET LEU PHE PRO GLU ALA ILE THR GLU LEU ALA MET TYR SEQRES 16 B 295 ARG GLN PHE ALA ASP ALA VAL GLN VAL PRO ILE LEU ALA SEQRES 17 B 295 ASN ILE THR GLU PHE GLY ALA THR PRO LEU PHE THR THR SEQRES 18 B 295 ASP GLU LEU ARG SER ALA HIS VAL ALA MET ALA LEU TYR SEQRES 19 B 295 PRO LEU SER ALA PHE ARG ALA MET ASN ARG ALA ALA GLU SEQRES 20 B 295 HIS VAL TYR ASN VAL LEU ARG GLN GLU GLY THR GLN LYS SEQRES 21 B 295 SER VAL ILE ASP THR MET GLN THR ARG ASN GLU LEU TYR SEQRES 22 B 295 GLU SER ILE ASN TYR TYR GLN TYR GLU GLU LYS LEU ASP SEQRES 23 B 295 ASN LEU PHE ALA ARG SER GLN VAL LYS SEQRES 1 C 295 SER LEU HIS SER PRO GLY LYS ALA PHE ARG ALA ALA LEU SEQRES 2 C 295 THR LYS GLU ASN PRO LEU GLN ILE VAL GLY THR ILE ASN SEQRES 3 C 295 ALA ASN HIS ALA LEU LEU ALA GLN ARG ALA GLY TYR GLN SEQRES 4 C 295 ALA ILE TYR LEU SER GLY GLY GLY VAL ALA ALA GLY SER SEQRES 5 C 295 LEU GLY LEU PRO ASP LEU GLY ILE SER THR LEU ASP ASP SEQRES 6 C 295 VAL LEU THR ASP ILE ARG ARG ILE THR ASP VAL CYS SER SEQRES 7 C 295 LEU PRO LEU LEU VAL ASP ALA ASP ILE GLY PHE GLY SER SEQRES 8 C 295 SER ALA PHE ASN VAL ALA ARG THR VAL LYS SER MET ILE SEQRES 9 C 295 LYS ALA GLY ALA ALA GLY LEU HIS ILE GLU ASP GLN VAL SEQRES 10 C 295 GLY ALA LYS ARG SER GLY HIS ARG PRO ASN LYS ALA ILE SEQRES 11 C 295 VAL SER LYS GLU GLU MET VAL ASP ARG ILE ARG ALA ALA SEQRES 12 C 295 VAL ASP ALA LYS THR ASP PRO ASP PHE VAL ILE MET ALA SEQRES 13 C 295 ARG THR ASP ALA LEU ALA VAL GLU GLY LEU ASP ALA ALA SEQRES 14 C 295 ILE GLU ARG ALA GLN ALA TYR VAL GLU ALA GLY ALA GLU SEQRES 15 C 295 MET LEU PHE PRO GLU ALA ILE THR GLU LEU ALA MET TYR SEQRES 16 C 295 ARG GLN PHE ALA ASP ALA VAL GLN VAL PRO ILE LEU ALA SEQRES 17 C 295 ASN ILE THR GLU PHE GLY ALA THR PRO LEU PHE THR THR SEQRES 18 C 295 ASP GLU LEU ARG SER ALA HIS VAL ALA MET ALA LEU TYR SEQRES 19 C 295 PRO LEU SER ALA PHE ARG ALA MET ASN ARG ALA ALA GLU SEQRES 20 C 295 HIS VAL TYR ASN VAL LEU ARG GLN GLU GLY THR GLN LYS SEQRES 21 C 295 SER VAL ILE ASP THR MET GLN THR ARG ASN GLU LEU TYR SEQRES 22 C 295 GLU SER ILE ASN TYR TYR GLN TYR GLU GLU LYS LEU ASP SEQRES 23 C 295 ASN LEU PHE ALA ARG SER GLN VAL LYS SEQRES 1 D 295 SER LEU HIS SER PRO GLY LYS ALA PHE ARG ALA ALA LEU SEQRES 2 D 295 THR LYS GLU ASN PRO LEU GLN ILE VAL GLY THR ILE ASN SEQRES 3 D 295 ALA ASN HIS ALA LEU LEU ALA GLN ARG ALA GLY TYR GLN SEQRES 4 D 295 ALA ILE TYR LEU SER GLY GLY GLY VAL ALA ALA GLY SER SEQRES 5 D 295 LEU GLY LEU PRO ASP LEU GLY ILE SER THR LEU ASP ASP SEQRES 6 D 295 VAL LEU THR ASP ILE ARG ARG ILE THR ASP VAL CYS SER SEQRES 7 D 295 LEU PRO LEU LEU VAL ASP ALA ASP ILE GLY PHE GLY SER SEQRES 8 D 295 SER ALA PHE ASN VAL ALA ARG THR VAL LYS SER MET ILE SEQRES 9 D 295 LYS ALA GLY ALA ALA GLY LEU HIS ILE GLU ASP GLN VAL SEQRES 10 D 295 GLY ALA LYS ARG SER GLY HIS ARG PRO ASN LYS ALA ILE SEQRES 11 D 295 VAL SER LYS GLU GLU MET VAL ASP ARG ILE ARG ALA ALA SEQRES 12 D 295 VAL ASP ALA LYS THR ASP PRO ASP PHE VAL ILE MET ALA SEQRES 13 D 295 ARG THR ASP ALA LEU ALA VAL GLU GLY LEU ASP ALA ALA SEQRES 14 D 295 ILE GLU ARG ALA GLN ALA TYR VAL GLU ALA GLY ALA GLU SEQRES 15 D 295 MET LEU PHE PRO GLU ALA ILE THR GLU LEU ALA MET TYR SEQRES 16 D 295 ARG GLN PHE ALA ASP ALA VAL GLN VAL PRO ILE LEU ALA SEQRES 17 D 295 ASN ILE THR GLU PHE GLY ALA THR PRO LEU PHE THR THR SEQRES 18 D 295 ASP GLU LEU ARG SER ALA HIS VAL ALA MET ALA LEU TYR SEQRES 19 D 295 PRO LEU SER ALA PHE ARG ALA MET ASN ARG ALA ALA GLU SEQRES 20 D 295 HIS VAL TYR ASN VAL LEU ARG GLN GLU GLY THR GLN LYS SEQRES 21 D 295 SER VAL ILE ASP THR MET GLN THR ARG ASN GLU LEU TYR SEQRES 22 D 295 GLU SER ILE ASN TYR TYR GLN TYR GLU GLU LYS LEU ASP SEQRES 23 D 295 ASN LEU PHE ALA ARG SER GLN VAL LYS HET MG A1101 1 HET ICT A1105 13 HET MG B1201 1 HET ICT B1205 13 HET MG D1401 1 HET ICT D1405 13 HETNAM MG MAGNESIUM ION HETNAM ICT ISOCITRIC ACID FORMUL 5 MG 3(MG 2+) FORMUL 6 ICT 3(C6 H8 O7) FORMUL 11 HOH *982(H2 O) HELIX 1 1 SER A 5 GLU A 17 1 13 HELIX 2 2 ASN A 27 ALA A 37 1 11 HELIX 3 3 SER A 45 GLY A 52 1 8 HELIX 4 4 THR A 63 CYS A 78 1 16 HELIX 5 5 SER A 93 GLY A 108 1 16 HELIX 6 6 SER A 133 LYS A 148 1 16 HELIX 7 7 ALA A 161 GLY A 166 1 6 HELIX 8 8 GLY A 166 ALA A 180 1 15 HELIX 9 9 GLU A 192 GLN A 204 1 13 HELIX 10 10 THR A 221 ALA A 228 1 8 HELIX 11 11 LEU A 237 GLY A 258 1 22 HELIX 12 12 GLN A 260 MET A 267 5 8 HELIX 13 13 THR A 269 ILE A 277 1 9 HELIX 14 14 ASN A 278 ASN A 288 1 11 HELIX 15 15 SER B 5 GLU B 17 1 13 HELIX 16 16 ASN B 27 ALA B 37 1 11 HELIX 17 17 SER B 45 GLY B 52 1 8 HELIX 18 18 THR B 63 CYS B 78 1 16 HELIX 19 19 SER B 93 GLY B 108 1 16 HELIX 20 20 SER B 133 LYS B 148 1 16 HELIX 21 21 ASP B 160 GLY B 166 1 7 HELIX 22 22 GLY B 166 ALA B 180 1 15 HELIX 23 23 GLU B 192 GLN B 204 1 13 HELIX 24 24 THR B 221 ALA B 228 1 8 HELIX 25 25 LEU B 237 GLY B 258 1 22 HELIX 26 26 GLN B 260 MET B 267 5 8 HELIX 27 27 THR B 269 ILE B 277 1 9 HELIX 28 28 ASN B 278 ASN B 288 1 11 HELIX 29 29 SER C 5 GLU C 17 1 13 HELIX 30 30 ASN C 27 ALA C 37 1 11 HELIX 31 31 SER C 45 GLY C 52 1 8 HELIX 32 32 THR C 63 CYS C 78 1 16 HELIX 33 33 SER C 93 GLY C 108 1 16 HELIX 34 34 SER C 133 ALA C 147 1 15 HELIX 35 35 ALA C 161 GLY C 166 1 6 HELIX 36 36 GLY C 166 ALA C 180 1 15 HELIX 37 37 GLU C 192 GLN C 204 1 13 HELIX 38 38 THR C 221 ALA C 228 1 8 HELIX 39 39 LEU C 237 GLY C 258 1 22 HELIX 40 40 GLN C 260 MET C 267 5 8 HELIX 41 41 THR C 269 ILE C 277 1 9 HELIX 42 42 ASN C 278 ASN C 288 1 11 HELIX 43 43 SER D 5 GLU D 17 1 13 HELIX 44 44 ASN D 27 ALA D 37 1 11 HELIX 45 45 SER D 45 GLY D 52 1 8 HELIX 46 46 THR D 63 CYS D 78 1 16 HELIX 47 47 SER D 93 GLY D 108 1 16 HELIX 48 48 SER D 133 LYS D 148 1 16 HELIX 49 49 ASP D 160 GLY D 166 1 7 HELIX 50 50 GLY D 166 ALA D 180 1 15 HELIX 51 51 GLU D 192 GLN D 204 1 13 HELIX 52 52 THR D 221 ALA D 228 1 8 HELIX 53 53 LEU D 237 GLY D 258 1 22 HELIX 54 54 GLN D 260 MET D 267 5 8 HELIX 55 55 THR D 269 ILE D 277 1 9 SHEET 1 A 8 MET A 184 PRO A 187 0 SHEET 2 A 8 VAL A 154 THR A 159 1 N ALA A 157 O PHE A 186 SHEET 3 A 8 GLY A 111 GLU A 115 1 N ILE A 114 O ARG A 158 SHEET 4 A 8 LEU A 82 ASP A 85 1 N VAL A 84 O GLY A 111 SHEET 5 A 8 ILE A 42 LEU A 44 1 N ILE A 42 O LEU A 83 SHEET 6 A 8 LEU A 20 GLY A 24 1 N VAL A 23 O TYR A 43 SHEET 7 A 8 MET A 232 TYR A 235 1 O ALA A 233 N ILE A 22 SHEET 8 A 8 LEU A 208 ASN A 210 1 N ALA A 209 O LEU A 234 SHEET 1 B 8 MET B 184 PRO B 187 0 SHEET 2 B 8 VAL B 154 THR B 159 1 N ALA B 157 O PHE B 186 SHEET 3 B 8 GLY B 111 GLU B 115 1 N LEU B 112 O MET B 156 SHEET 4 B 8 LEU B 82 ASP B 85 1 N VAL B 84 O GLY B 111 SHEET 5 B 8 ILE B 42 LEU B 44 1 N ILE B 42 O LEU B 83 SHEET 6 B 8 LEU B 20 GLY B 24 1 N VAL B 23 O TYR B 43 SHEET 7 B 8 MET B 232 TYR B 235 1 O ALA B 233 N ILE B 22 SHEET 8 B 8 LEU B 208 ASN B 210 1 N ALA B 209 O LEU B 234 SHEET 1 C 8 MET C 184 PRO C 187 0 SHEET 2 C 8 VAL C 154 THR C 159 1 N ALA C 157 O PHE C 186 SHEET 3 C 8 GLY C 111 GLU C 115 1 N LEU C 112 O MET C 156 SHEET 4 C 8 LEU C 82 ASP C 85 1 N VAL C 84 O GLY C 111 SHEET 5 C 8 ILE C 42 LEU C 44 1 N ILE C 42 O LEU C 83 SHEET 6 C 8 LEU C 20 GLY C 24 1 N VAL C 23 O TYR C 43 SHEET 7 C 8 MET C 232 TYR C 235 1 O ALA C 233 N ILE C 22 SHEET 8 C 8 LEU C 208 ASN C 210 1 N ALA C 209 O LEU C 234 SHEET 1 D 8 MET D 184 PRO D 187 0 SHEET 2 D 8 VAL D 154 THR D 159 1 N ALA D 157 O PHE D 186 SHEET 3 D 8 GLY D 111 GLU D 115 1 N LEU D 112 O MET D 156 SHEET 4 D 8 LEU D 82 ASP D 85 1 N VAL D 84 O GLY D 111 SHEET 5 D 8 ILE D 42 LEU D 44 1 N ILE D 42 O LEU D 83 SHEET 6 D 8 LEU D 20 GLY D 24 1 N VAL D 23 O TYR D 43 SHEET 7 D 8 MET D 232 TYR D 235 1 O ALA D 233 N ILE D 22 SHEET 8 D 8 LEU D 208 ASN D 210 1 N ALA D 209 O LEU D 234 LINK OD2 ASP A 85 MG MG A1101 1555 1555 2.19 LINK MG MG A1101 O7 ICT A1105 1555 1555 2.62 LINK MG MG A1101 O2 ICT A1105 1555 1555 2.43 LINK MG MG A1101 O HOH A1360 1555 1555 2.11 LINK MG MG A1101 O HOH A1361 1555 1555 2.40 LINK MG MG A1101 O HOH A1362 1555 1555 2.44 LINK OD2 ASP B 85 MG MG B1201 1555 1555 2.00 LINK MG MG B1201 O2 ICT B1205 1555 1555 2.40 LINK MG MG B1201 O7 ICT B1205 1555 1555 2.66 LINK MG MG B1201 O HOH B1465 1555 1555 2.33 LINK MG MG B1201 O HOH B1466 1555 1555 2.46 LINK MG MG B1201 O HOH B1467 1555 1555 2.30 LINK OD2 ASP D 85 MG MG D1401 1555 1555 2.06 LINK MG MG D1401 O2 ICT D1405 1555 1555 2.41 LINK MG MG D1401 O7 ICT D1405 1555 1555 2.61 LINK MG MG D1401 O HOH D1633 1555 1555 2.32 LINK MG MG D1401 O HOH D1634 1555 1555 2.37 LINK MG MG D1401 O HOH D1635 1555 1555 2.33 CISPEP 1 ASN A 18 PRO A 19 0 0.00 CISPEP 2 ASN B 18 PRO B 19 0 -0.15 CISPEP 3 ASN C 18 PRO C 19 0 0.05 CISPEP 4 ASN D 18 PRO D 19 0 -0.21 SITE 1 AC1 5 ASP A 85 ICT A1105 HOH A1360 HOH A1361 SITE 2 AC1 5 HOH A1362 SITE 1 AC2 5 ASP B 85 ICT B1205 HOH B1465 HOH B1466 SITE 2 AC2 5 HOH B1467 SITE 1 AC3 5 ASP D 85 ICT D1405 HOH D1633 HOH D1634 SITE 2 AC3 5 HOH D1635 SITE 1 AC4 16 SER A 45 GLY A 46 GLY A 47 ASP A 85 SITE 2 AC4 16 SER A 123 GLY A 124 HIS A 125 ARG A 158 SITE 3 AC4 16 GLU A 188 ASN A 210 THR A 212 PRO A 236 SITE 4 AC4 16 ARG A 241 MG A1101 HOH A1360 ARG B 270 SITE 1 AC5 17 ARG A 270 SER B 45 GLY B 46 GLY B 47 SITE 2 AC5 17 ASP B 85 SER B 123 GLY B 124 HIS B 125 SITE 3 AC5 17 ARG B 158 GLU B 188 ASN B 210 THR B 212 SITE 4 AC5 17 PRO B 236 ARG B 241 MG B1201 HOH B1230 SITE 5 AC5 17 HOH B1465 SITE 1 AC6 17 ARG C 270 SER D 45 GLY D 46 GLY D 47 SITE 2 AC6 17 ASP D 85 SER D 123 GLY D 124 HIS D 125 SITE 3 AC6 17 ARG D 158 GLU D 188 ASN D 210 THR D 212 SITE 4 AC6 17 PRO D 236 ARG D 241 MG D1401 HOH D1436 SITE 5 AC6 17 HOH D1633 CRYST1 159.061 84.561 99.756 90.00 108.15 90.00 C 1 2 1 16 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 0.006287 0.000000 0.002061 0.00000 SCALE2 0.000000 0.011826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010549 0.00000