10 20 30 40 50 60 70 80 1XG4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE 16-SEP-04 1XG4
TITLE CRYSTAL STRUCTURE OF THE C123S 2-METHYLISOCITRATE LYASE TITLE 2 MUTANT FROM ESCHERICHIA COLI IN COMPLEX WITH THE INHIBITOR TITLE 3 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, KEYWDS 2 ISOCITRATE LYASE SUPERFAMILY
EXPDTA X-RAY DIFFRACTION
AUTHOR S.LIU,Z.LU,Y.HAN,E.MELAMUD,D.DUNAWAY-MARIANO,O.HERZBERG
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, JRNL AUTH 2 O.HERZBERG JRNL TITL CRYSTAL STRUCTURES OF 2-METHYLISOCITRATE LYASE IN JRNL TITL 2 COMPLEX WITH PRODUCT AND WITH ISOCITRATE INHIBITOR JRNL TITL 3 PROVIDE INSIGHT INTO LYASE SUBSTRATE SPECIFICITY, JRNL TITL 4 CATALYSIS AND EVOLUTION JRNL REF BIOCHEMISTRY V. 44 2949 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15723538 JRNL DOI 10.1021/BI0479712
REMARK 1
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 : 51 REMARK 3 SOLVENT ATOMS : 973 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) : 1.30 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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-04. REMARK 100 THE RCSB ID CODE IS RCSB030325.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 REMARK 280 MES (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 REMARK 300 BIOLOGICAL 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 HOH A1360 O REMARK 620 2 HOH A1361 O 90.0 REMARK 620 3 HOH A1362 O 94.0 99.1 REMARK 620 4 ICT A1105 O7 82.3 164.4 95.0 REMARK 620 5 ICT A1105 O2 99.6 102.8 154.1 65.5 REMARK 620 6 ASP A 85 OD2 169.7 89.7 76.0 100.2 90.4 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 HOH B1467 O REMARK 620 2 HOH B1465 O 88.9 REMARK 620 3 HOH B1466 O 94.0 83.8 REMARK 620 4 ICT B1205 O2 157.9 96.2 107.8 REMARK 620 5 ASP B 85 OD2 78.2 166.3 92.4 97.5 REMARK 620 6 ICT B1205 O7 93.4 82.3 164.1 66.2 102.9 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 HOH D1634 O REMARK 620 2 HOH D1635 O 98.0 REMARK 620 3 HOH D1633 O 82.9 94.3 REMARK 620 4 ICT D1405 O2 101.8 159.0 95.0 REMARK 620 5 ICT D1405 O7 162.5 95.4 85.0 66.7 REMARK 620 6 ASP D 85 OD2 91.7 78.3 170.2 94.2 102.0 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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1201 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 1401 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT A 1105 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT B 1205 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)- REMARK 900 PYRUVATE 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 SEQADV 1XG4 SER B 123 UNP P77541 CYS 122 ENGINEERED SEQADV 1XG4 SER C 123 UNP P77541 CYS 122 ENGINEERED SEQADV 1XG4 SER D 123 UNP P77541 CYS 122 ENGINEERED
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 MG B1201 1 HET MG D1401 1 HET ICT A1105 13 HET ICT B1205 13 HET ICT D1405 13
HETNAM MG MAGNESIUM ION HETNAM ICT ISOCITRIC ACID
FORMUL 5 MG 3(MG 2+) FORMUL 8 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 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 MG MG B1201 O HOH B1467 1555 1555 2.30 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 D1401 O HOH D1634 1555 1555 2.37 LINK MG MG D1401 O HOH D1635 1555 1555 2.33 LINK MG MG D1401 O HOH D1633 1555 1555 2.32 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 OD2 ASP A 85 1555 1555 2.19 LINK MG MG B1201 O2 ICT B1205 1555 1555 2.40 LINK MG MG B1201 OD2 ASP B 85 1555 1555 2.00 LINK MG MG B1201 O7 ICT B1205 1555 1555 2.66 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 OD2 ASP D 85 1555 1555 2.06
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