HEADER OXIDOREDUCTASE 01-FEB-05 2BJA TITLE CRYSTAL ANALYSIS OF 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM TITLE 2 THERMUS WITH BOUND NADH COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.5.1.12; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: OXIDATION OF CYS TO CSO (S-HYDROXYL -CYSTEINE) AT A COMPND 7 322 AND B 322 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PET11A KEYWDS 1-PYRROLINE-5-CARBOXYLATE, DEHYROGENASE, OXIDOREDUCTASE, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR E.INAGAKI,T.H.TAHIROV REVDAT 6 13-DEC-23 2BJA 1 LINK REVDAT 5 24-FEB-09 2BJA 1 VERSN REVDAT 4 14-SEP-06 2BJA 1 REVDAT REVDAT 3 06-SEP-06 2BJA 1 JRNL REVDAT 2 30-AUG-06 2BJA 1 JRNL REVDAT 1 09-MAR-06 2BJA 0 JRNL AUTH E.INAGAKI,N.OHSHIMA,H.TAKAHASHI,C.KUROISHI,S.YOKOYAMA, JRNL AUTH 2 T.H.TAHIROV JRNL TITL CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS JRNL TITL 2 DELTA1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE. JRNL REF J.MOL.BIOL. V. 362 490 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16934832 JRNL DOI 10.1016/J.JMB.2006.07.048 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 397651.160 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 82153 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) : 0.176 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4178 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 12060 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 650 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8075 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 808 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.15000 REMARK 3 B22 (A**2) : 6.15000 REMARK 3 B33 (A**2) : -12.30000 REMARK 3 B12 (A**2) : 3.96000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.110 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.540 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.900 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 80.59 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_OCYS_REP_CSO014.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 5 : SOL.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_OCYS_CSO014.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : SOL.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THERE ARE CISPEPS AT A154-155 AND B154 REMARK 3 -155.NAHS ARE DISORDERED. MOST PARTS OF DISORDERED REGIONS OF REMARK 3 NAHS COULD NOT BE MODELED. REMARK 4 REMARK 4 2BJA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1290022787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 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 : SILICON CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85247 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1UZB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 36% MPD, REMARK 280 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN 1 MM NAD,CA.5MM REMARK 280 DELTA1-PYRROLINE-5 CARBOXYLATE AND 50 MM SODIUM ACETATE/HCL, PH REMARK 280 5.2. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.00350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.44688 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 92.77300 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 51.00350 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 29.44688 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 92.77300 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 51.00350 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 29.44688 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 92.77300 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.89377 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 185.54600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 58.89377 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 185.54600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 58.89377 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 185.54600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 33640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 118090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -118.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -0.500000 -0.866025 0.000000 102.00700 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 51.00350 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 88.34065 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 MET A 1 CG SD CE 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 ALA A 60 76.63 -169.92 REMARK 500 PRO A 61 -3.94 -53.92 REMARK 500 GLU A 242 -86.58 -109.26 REMARK 500 GLN A 320 58.44 -92.78 REMARK 500 GLN A 415 -36.59 -134.67 REMARK 500 LEU A 445 -74.34 -95.13 REMARK 500 LYS A 489 -135.40 50.10 REMARK 500 ALA B 60 72.70 -170.89 REMARK 500 GLU B 242 -85.69 -92.46 REMARK 500 LEU B 445 -77.73 -90.28 REMARK 500 LYS B 489 -134.68 51.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2068 DISTANCE = 6.42 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAD A 1517 REMARK 610 NAD B 1517 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1519 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1519 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A1517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A1520 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B1517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B1520 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BHP RELATED DB: PDB REMARK 900 CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM REMARK 900 THERMUS WITH BOUND NAD. REMARK 900 RELATED ID: 2BHQ RELATED DB: PDB REMARK 900 CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM REMARK 900 THERMUS WITH BOUND PRODUCT GLUTAMATE. REMARK 900 RELATED ID: 2BJK RELATED DB: PDB REMARK 900 CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM REMARK 900 THERMUS WITH BOUND NAD AND CITRATE. DBREF 2BJA A 1 516 UNP Q5SI02 Q5SI02_THET8 1 516 DBREF 2BJA B 1 516 UNP Q5SI02 Q5SI02_THET8 1 516 SEQRES 1 A 516 MET THR VAL GLU PRO PHE ARG ASN GLU PRO ILE GLU THR SEQRES 2 A 516 PHE GLN THR GLU GLU ALA ARG ARG ALA MET ARG GLU ALA SEQRES 3 A 516 LEU ARG ARG VAL ARG GLU GLU PHE GLY ARG HIS TYR PRO SEQRES 4 A 516 LEU TYR ILE GLY GLY GLU TRP VAL ASP THR LYS GLU ARG SEQRES 5 A 516 MET VAL SER LEU ASN PRO SER ALA PRO SER GLU VAL VAL SEQRES 6 A 516 GLY THR THR ALA LYS ALA GLY LYS ALA GLU ALA GLU ALA SEQRES 7 A 516 ALA LEU GLU ALA ALA TRP LYS ALA PHE LYS THR TRP LYS SEQRES 8 A 516 ASP TRP PRO GLN GLU ASP ARG SER ARG LEU LEU LEU LYS SEQRES 9 A 516 ALA ALA ALA LEU MET ARG ARG ARG LYS ARG GLU LEU GLU SEQRES 10 A 516 ALA THR LEU VAL TYR GLU VAL GLY LYS ASN TRP VAL GLU SEQRES 11 A 516 ALA SER ALA ASP VAL ALA GLU ALA ILE ASP PHE ILE GLU SEQRES 12 A 516 TYR TYR ALA ARG ALA ALA LEU ARG TYR ARG TYR PRO ALA SEQRES 13 A 516 VAL GLU VAL VAL PRO TYR PRO GLY GLU ASP ASN GLU SER SEQRES 14 A 516 PHE TYR VAL PRO LEU GLY ALA GLY VAL VAL ILE ALA PRO SEQRES 15 A 516 TRP ASN PHE PRO VAL ALA ILE PHE THR GLY MET ILE VAL SEQRES 16 A 516 GLY PRO VAL ALA VAL GLY ASN THR VAL ILE ALA LYS PRO SEQRES 17 A 516 ALA GLU ASP ALA VAL VAL VAL GLY ALA LYS VAL PHE GLU SEQRES 18 A 516 ILE PHE HIS GLU ALA GLY PHE PRO PRO GLY VAL VAL ASN SEQRES 19 A 516 PHE LEU PRO GLY VAL GLY GLU GLU VAL GLY ALA TYR LEU SEQRES 20 A 516 VAL GLU HIS PRO ARG ILE ARG PHE ILE ASN PHE THR GLY SEQRES 21 A 516 SER LEU GLU VAL GLY LEU LYS ILE TYR GLU ALA ALA GLY SEQRES 22 A 516 ARG LEU ALA PRO GLY GLN THR TRP PHE LYS ARG ALA TYR SEQRES 23 A 516 VAL GLU THR GLY GLY LYS ASP ALA ILE ILE VAL ASP GLU SEQRES 24 A 516 THR ALA ASP PHE ASP LEU ALA ALA GLU GLY VAL VAL VAL SEQRES 25 A 516 SER ALA TYR GLY PHE GLN GLY GLN LYS CSO SER ALA ALA SEQRES 26 A 516 SER ARG LEU ILE LEU THR GLN GLY ALA TYR GLU PRO VAL SEQRES 27 A 516 LEU GLU ARG VAL LEU LYS ARG ALA GLU ARG LEU SER VAL SEQRES 28 A 516 GLY PRO ALA GLU GLU ASN PRO ASP LEU GLY PRO VAL VAL SEQRES 29 A 516 SER ALA GLU GLN GLU ARG LYS VAL LEU SER TYR ILE GLU SEQRES 30 A 516 ILE GLY LYS ASN GLU GLY GLN LEU VAL LEU GLY GLY LYS SEQRES 31 A 516 ARG LEU GLU GLY GLU GLY TYR PHE ILE ALA PRO THR VAL SEQRES 32 A 516 PHE THR GLU VAL PRO PRO LYS ALA ARG ILE ALA GLN GLU SEQRES 33 A 516 GLU ILE PHE GLY PRO VAL LEU SER VAL ILE ARG VAL LYS SEQRES 34 A 516 ASP PHE ALA GLU ALA LEU GLU VAL ALA ASN ASP THR PRO SEQRES 35 A 516 TYR GLY LEU THR GLY GLY VAL TYR SER ARG LYS ARG GLU SEQRES 36 A 516 HIS LEU GLU TRP ALA ARG ARG GLU PHE HIS VAL GLY ASN SEQRES 37 A 516 LEU TYR PHE ASN ARG LYS ILE THR GLY ALA LEU VAL GLY SEQRES 38 A 516 VAL GLN PRO PHE GLY GLY PHE LYS LEU SER GLY THR ASN SEQRES 39 A 516 ALA LYS THR GLY ALA LEU ASP TYR LEU ARG LEU PHE LEU SEQRES 40 A 516 GLU MET LYS ALA VAL ALA GLU ARG PHE SEQRES 1 B 516 MET THR VAL GLU PRO PHE ARG ASN GLU PRO ILE GLU THR SEQRES 2 B 516 PHE GLN THR GLU GLU ALA ARG ARG ALA MET ARG GLU ALA SEQRES 3 B 516 LEU ARG ARG VAL ARG GLU GLU PHE GLY ARG HIS TYR PRO SEQRES 4 B 516 LEU TYR ILE GLY GLY GLU TRP VAL ASP THR LYS GLU ARG SEQRES 5 B 516 MET VAL SER LEU ASN PRO SER ALA PRO SER GLU VAL VAL SEQRES 6 B 516 GLY THR THR ALA LYS ALA GLY LYS ALA GLU ALA GLU ALA SEQRES 7 B 516 ALA LEU GLU ALA ALA TRP LYS ALA PHE LYS THR TRP LYS SEQRES 8 B 516 ASP TRP PRO GLN GLU ASP ARG SER ARG LEU LEU LEU LYS SEQRES 9 B 516 ALA ALA ALA LEU MET ARG ARG ARG LYS ARG GLU LEU GLU SEQRES 10 B 516 ALA THR LEU VAL TYR GLU VAL GLY LYS ASN TRP VAL GLU SEQRES 11 B 516 ALA SER ALA ASP VAL ALA GLU ALA ILE ASP PHE ILE GLU SEQRES 12 B 516 TYR TYR ALA ARG ALA ALA LEU ARG TYR ARG TYR PRO ALA SEQRES 13 B 516 VAL GLU VAL VAL PRO TYR PRO GLY GLU ASP ASN GLU SER SEQRES 14 B 516 PHE TYR VAL PRO LEU GLY ALA GLY VAL VAL ILE ALA PRO SEQRES 15 B 516 TRP ASN PHE PRO VAL ALA ILE PHE THR GLY MET ILE VAL SEQRES 16 B 516 GLY PRO VAL ALA VAL GLY ASN THR VAL ILE ALA LYS PRO SEQRES 17 B 516 ALA GLU ASP ALA VAL VAL VAL GLY ALA LYS VAL PHE GLU SEQRES 18 B 516 ILE PHE HIS GLU ALA GLY PHE PRO PRO GLY VAL VAL ASN SEQRES 19 B 516 PHE LEU PRO GLY VAL GLY GLU GLU VAL GLY ALA TYR LEU SEQRES 20 B 516 VAL GLU HIS PRO ARG ILE ARG PHE ILE ASN PHE THR GLY SEQRES 21 B 516 SER LEU GLU VAL GLY LEU LYS ILE TYR GLU ALA ALA GLY SEQRES 22 B 516 ARG LEU ALA PRO GLY GLN THR TRP PHE LYS ARG ALA TYR SEQRES 23 B 516 VAL GLU THR GLY GLY LYS ASP ALA ILE ILE VAL ASP GLU SEQRES 24 B 516 THR ALA ASP PHE ASP LEU ALA ALA GLU GLY VAL VAL VAL SEQRES 25 B 516 SER ALA TYR GLY PHE GLN GLY GLN LYS CSO SER ALA ALA SEQRES 26 B 516 SER ARG LEU ILE LEU THR GLN GLY ALA TYR GLU PRO VAL SEQRES 27 B 516 LEU GLU ARG VAL LEU LYS ARG ALA GLU ARG LEU SER VAL SEQRES 28 B 516 GLY PRO ALA GLU GLU ASN PRO ASP LEU GLY PRO VAL VAL SEQRES 29 B 516 SER ALA GLU GLN GLU ARG LYS VAL LEU SER TYR ILE GLU SEQRES 30 B 516 ILE GLY LYS ASN GLU GLY GLN LEU VAL LEU GLY GLY LYS SEQRES 31 B 516 ARG LEU GLU GLY GLU GLY TYR PHE ILE ALA PRO THR VAL SEQRES 32 B 516 PHE THR GLU VAL PRO PRO LYS ALA ARG ILE ALA GLN GLU SEQRES 33 B 516 GLU ILE PHE GLY PRO VAL LEU SER VAL ILE ARG VAL LYS SEQRES 34 B 516 ASP PHE ALA GLU ALA LEU GLU VAL ALA ASN ASP THR PRO SEQRES 35 B 516 TYR GLY LEU THR GLY GLY VAL TYR SER ARG LYS ARG GLU SEQRES 36 B 516 HIS LEU GLU TRP ALA ARG ARG GLU PHE HIS VAL GLY ASN SEQRES 37 B 516 LEU TYR PHE ASN ARG LYS ILE THR GLY ALA LEU VAL GLY SEQRES 38 B 516 VAL GLN PRO PHE GLY GLY PHE LYS LEU SER GLY THR ASN SEQRES 39 B 516 ALA LYS THR GLY ALA LEU ASP TYR LEU ARG LEU PHE LEU SEQRES 40 B 516 GLU MET LYS ALA VAL ALA GLU ARG PHE MODRES 2BJA CSO A 322 CYS S-HYDROXYCYSTEINE MODRES 2BJA CSO B 322 CYS S-HYDROXYCYSTEINE HET CSO A 322 9 HET CSO B 322 9 HET NAD A1517 34 HET ACT A1518 4 HET CL A1519 1 HET MRD A1520 8 HET NAD B1517 27 HET ACT B1518 4 HET CL B1519 1 HET MPD B1520 8 HETNAM CSO S-HYDROXYCYSTEINE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 5 CL 2(CL 1-) FORMUL 6 MRD C6 H14 O2 FORMUL 10 MPD C6 H14 O2 FORMUL 11 HOH *808(H2 O) HELIX 1 1 THR A 16 GLU A 32 1 17 HELIX 2 2 GLY A 72 LYS A 91 1 20 HELIX 3 3 PRO A 94 ARG A 112 1 19 HELIX 4 4 ARG A 112 GLY A 125 1 14 HELIX 5 5 ASN A 127 ARG A 151 1 25 HELIX 6 6 VAL A 187 VAL A 200 1 14 HELIX 7 7 ALA A 209 ASP A 211 5 3 HELIX 8 8 ALA A 212 GLY A 227 1 16 HELIX 9 9 GLU A 242 HIS A 250 1 9 HELIX 10 10 SER A 261 GLY A 273 1 13 HELIX 11 11 ASP A 302 GLY A 316 1 15 HELIX 12 12 PHE A 317 GLN A 320 5 4 HELIX 13 13 ALA A 334 GLU A 347 1 14 HELIX 14 14 PRO A 353 ASN A 357 5 5 HELIX 15 15 SER A 365 ASN A 381 1 17 HELIX 16 16 ALA A 411 GLN A 415 5 5 HELIX 17 17 ASP A 430 ASP A 440 1 11 HELIX 18 18 LYS A 453 PHE A 464 1 12 HELIX 19 19 PHE A 488 SER A 491 5 4 HELIX 20 20 ALA A 499 LEU A 505 1 7 HELIX 21 21 THR B 16 GLU B 32 1 17 HELIX 22 22 GLY B 72 LYS B 91 1 20 HELIX 23 23 PRO B 94 ARG B 112 1 19 HELIX 24 24 ARG B 112 GLY B 125 1 14 HELIX 25 25 ASN B 127 LEU B 150 1 24 HELIX 26 26 ARG B 151 ARG B 153 5 3 HELIX 27 27 VAL B 187 VAL B 200 1 14 HELIX 28 28 ALA B 209 ASP B 211 5 3 HELIX 29 29 ALA B 212 GLY B 227 1 16 HELIX 30 30 GLU B 242 HIS B 250 1 9 HELIX 31 31 SER B 261 GLY B 273 1 13 HELIX 32 32 ASP B 302 GLY B 316 1 15 HELIX 33 33 PHE B 317 GLN B 320 5 4 HELIX 34 34 ALA B 334 GLU B 347 1 14 HELIX 35 35 PRO B 353 ASN B 357 5 5 HELIX 36 36 SER B 365 GLY B 383 1 19 HELIX 37 37 ALA B 411 GLN B 415 5 5 HELIX 38 38 ASP B 430 ASP B 440 1 11 HELIX 39 39 LYS B 453 PHE B 464 1 12 HELIX 40 40 PHE B 488 SER B 491 5 4 HELIX 41 41 ALA B 499 LEU B 505 1 7 SHEET 1 AA 3 ARG A 36 TYR A 38 0 SHEET 2 AA 3 VAL A 64 ALA A 69 1 O THR A 67 N TYR A 38 SHEET 3 AA 3 ARG A 52 LEU A 56 -1 O MET A 53 N THR A 68 SHEET 1 AB 2 LEU A 40 ILE A 42 0 SHEET 2 AB 2 GLU A 45 VAL A 47 -1 O GLU A 45 N ILE A 42 SHEET 1 AC 9 GLU A 165 PRO A 173 0 SHEET 2 AC 9 LEU A 507 ARG A 515 -1 O GLU A 508 N VAL A 172 SHEET 3 AC 9 ASN B 468 PHE B 471 1 O LEU B 469 N ALA A 513 SHEET 4 AC 9 THR B 446 TYR B 450 1 O GLY B 447 N TYR B 470 SHEET 5 AC 9 ASP B 293 VAL B 297 1 O ALA B 294 N GLY B 448 SHEET 6 AC 9 ALA B 325 THR B 331 1 N SER B 326 O ASP B 293 SHEET 7 AC 9 VAL B 422 VAL B 428 1 O SER B 424 N LEU B 328 SHEET 8 AC 9 THR B 402 THR B 405 1 O THR B 402 N LEU B 423 SHEET 9 AC 9 GLN B 384 LEU B 387 -1 O GLN B 384 N THR B 405 SHEET 1 AD 5 VAL A 233 PHE A 235 0 SHEET 2 AD 5 THR A 203 LYS A 207 1 O VAL A 204 N ASN A 234 SHEET 3 AD 5 ALA A 176 ILE A 180 1 O GLY A 177 N ILE A 205 SHEET 4 AD 5 PHE A 255 THR A 259 1 O PHE A 255 N VAL A 178 SHEET 5 AD 5 ARG A 284 GLU A 288 1 O ARG A 284 N ILE A 256 SHEET 1 AE 9 GLN A 384 LEU A 387 0 SHEET 2 AE 9 THR A 402 THR A 405 -1 O VAL A 403 N VAL A 386 SHEET 3 AE 9 VAL A 422 VAL A 428 1 O LEU A 423 N PHE A 404 SHEET 4 AE 9 ALA A 325 THR A 331 1 O SER A 326 N SER A 424 SHEET 5 AE 9 ASP A 293 VAL A 297 1 O ASP A 293 N SER A 326 SHEET 6 AE 9 THR A 446 TYR A 450 1 O THR A 446 N ALA A 294 SHEET 7 AE 9 ASN A 468 PHE A 471 1 O ASN A 468 N GLY A 447 SHEET 8 AE 9 LEU B 507 ARG B 515 1 O ALA B 511 N LEU A 469 SHEET 9 AE 9 GLU B 165 PRO B 173 -1 O ASP B 166 N GLU B 514 SHEET 1 BA 3 HIS B 37 TYR B 38 0 SHEET 2 BA 3 ALA B 60 ALA B 69 1 O THR B 67 N TYR B 38 SHEET 3 BA 3 ARG B 52 ASN B 57 -1 O MET B 53 N THR B 68 SHEET 1 BB 2 LEU B 40 ILE B 42 0 SHEET 2 BB 2 GLU B 45 VAL B 47 -1 O GLU B 45 N ILE B 42 SHEET 1 BC 5 VAL B 233 PHE B 235 0 SHEET 2 BC 5 THR B 203 LYS B 207 1 O VAL B 204 N ASN B 234 SHEET 3 BC 5 ALA B 176 ILE B 180 1 O GLY B 177 N ILE B 205 SHEET 4 BC 5 PHE B 255 THR B 259 1 O PHE B 255 N VAL B 178 SHEET 5 BC 5 ARG B 284 GLU B 288 1 O ARG B 284 N ILE B 256 LINK C LYS A 321 N CSO A 322 1555 1555 1.33 LINK C CSO A 322 N SER A 323 1555 1555 1.33 LINK C LYS B 321 N CSO B 322 1555 1555 1.33 LINK C CSO B 322 N SER B 323 1555 1555 1.33 CISPEP 1 TYR A 154 PRO A 155 0 -3.67 CISPEP 2 TYR B 154 PRO B 155 0 -1.40 SITE 1 AC1 2 HIS A 465 LYS B 510 SITE 1 AC2 2 LYS A 510 HIS B 465 SITE 1 AC3 17 ILE A 180 ALA A 181 TRP A 183 LYS A 207 SITE 2 AC3 17 ALA A 209 GLU A 210 GLY A 240 GLU A 241 SITE 3 AC3 17 ALA A 245 PHE A 258 SER A 261 VAL A 264 SITE 4 AC3 17 ACT A1518 HOH A2411 HOH A2412 HOH A2413 SITE 5 AC3 17 HOH A2414 SITE 1 AC4 5 ALA A 245 GLU A 249 LYS A 267 ALA A 271 SITE 2 AC4 5 NAD A1517 SITE 1 AC5 10 PHE A 6 TYR A 144 ARG A 147 ALA A 148 SITE 2 AC5 10 HOH A2009 HOH A2161 HOH A2415 HOH A2416 SITE 3 AC5 10 GLU B 158 VAL B 160 SITE 1 AC6 16 ILE B 180 ALA B 181 TRP B 183 LYS B 207 SITE 2 AC6 16 ALA B 209 GLU B 210 GLY B 240 GLY B 244 SITE 3 AC6 16 ALA B 245 PHE B 258 SER B 261 VAL B 264 SITE 4 AC6 16 ACT B1518 HOH B2388 HOH B2389 HOH B2390 SITE 1 AC7 5 ALA B 245 GLU B 249 ILE B 268 ALA B 271 SITE 2 AC7 5 NAD B1517 SITE 1 AC8 9 GLU A 158 HOH A2181 PHE B 6 TYR B 144 SITE 2 AC8 9 ARG B 147 ALA B 148 HOH B2146 HOH B2391 SITE 3 AC8 9 HOH B2392 CRYST1 102.007 102.007 278.319 90.00 90.00 120.00 H 3 18 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 0.009803 0.005660 0.000000 0.00000 SCALE2 0.000000 0.011320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003593 0.00000 MTRIX1 1 0.976560 -0.215210 -0.004160 7.97701 1 MTRIX2 1 -0.215210 -0.976570 0.000110 69.13280 1 MTRIX3 1 -0.004090 0.000790 -0.999990 222.82058 1