HEADER HYDROLASE 09-MAY-01 1IM5 TITLE CRYSTAL STRUCTURE OF PYRAZINAMIDASE OF PYROCOCCUS HORIKOSHII IN TITLE 2 COMPLEX WITH ZINC COMPND MOL_ID: 1; COMPND 2 MOLECULE: 180AA LONG HYPOTHETICAL PYRAZINAMIDASE/NICOTINAMIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.1.19; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 GENE: PH 999; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3)/SJS1244; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS PYRAZINAMIDASE, PYRAZINAMIDE, NICOTINAMIDASE, TUBERCULOSIS, PZA KEYWDS 2 RESISTANCE, DRUG RESISTANCE, METAL ION CATALYSIS, CYSTEINE KEYWDS 3 HYDROLASE, HYDROLASE, AMIDASE, COVALENT CATALYSIS EXPDTA X-RAY DIFFRACTION AUTHOR X.DU,S.-H.KIM REVDAT 6 03-APR-24 1IM5 1 REMARK REVDAT 5 07-FEB-24 1IM5 1 REMARK LINK REVDAT 4 24-JUL-19 1IM5 1 REMARK REVDAT 3 04-OCT-17 1IM5 1 REMARK REVDAT 2 24-FEB-09 1IM5 1 VERSN REVDAT 1 12-DEC-01 1IM5 0 JRNL AUTH X.DU,W.WANG,R.KIM,H.YAKOTA,H.NGUYEN,S.H.KIM JRNL TITL CRYSTAL STRUCTURE AND MECHANISM OF CATALYSIS OF A JRNL TITL 2 PYRAZINAMIDASE FROM PYROCOCCUS HORIKOSHII. JRNL REF BIOCHEMISTRY V. 40 14166 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11714269 JRNL DOI 10.1021/BI0115479 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.152 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1775 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 18533 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.152 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 16030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1413 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1552.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14202 REMARK 3 NUMBER OF RESTRAINTS : 17019 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.000 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.025 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.030 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.050 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.050 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 1IM5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000013404. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18049 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.110 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 37.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.02 REMARK 200 R MERGE FOR SHELL (I) : 0.06400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 25.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE, CNS 0.5 REMARK 200 STARTING MODEL: A STRUCTURE OBTAINED ON MAD DATA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27.5% PEG 3350, 100MM SODIUM ACETATE, REMARK 280 PH 4.6, 250 MM AMMONIUM ACETATE, 8% GLYCEROL. SEEDING., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K. PEG 3350, AMMONIUM REMARK 280 ACETATE, SODIUM ACETATE, GLYCEROL, PH 4.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 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 21.63300 REMARK 290 SMTRY3 2 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: MONOMER IS BIOLOGICALLY ACTIVE 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 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 64 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES 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 TYR A 132 -101.15 -117.09 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 ZN A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 52 OD2 REMARK 620 2 HIS A 54 NE2 90.5 REMARK 620 3 HIS A 71 NE2 98.1 94.7 REMARK 620 4 HOH A 203 O 167.7 94.7 92.6 REMARK 620 5 HOH A 214 O 83.6 167.8 96.7 89.1 REMARK 620 6 HOH A 223 O 83.2 93.5 171.7 85.4 75.2 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 ZN A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ILW RELATED DB: PDB REMARK 900 1ILW IS THE CRYSTAL STRUCTURE OF PYRAZINAMIDASE/NICOTINAMIDASE OF REMARK 900 PYROCOCCUS HORIKOSHII DBREF 1IM5 A 1 180 UNP O58727 O58727_PYRHO 1 180 SEQRES 1 A 180 MET PRO GLU GLU ALA LEU ILE VAL VAL ASP MET GLN ARG SEQRES 2 A 180 ASP PHE MET PRO GLY GLY ALA LEU PRO VAL PRO GLU GLY SEQRES 3 A 180 ASP LYS ILE ILE PRO LYS VAL ASN GLU TYR ILE ARG LYS SEQRES 4 A 180 PHE LYS GLU LYS GLY ALA LEU ILE VAL ALA THR ARG ASP SEQRES 5 A 180 TRP HIS PRO GLU ASN HIS ILE SER PHE ARG GLU ARG GLY SEQRES 6 A 180 GLY PRO TRP PRO ARG HIS CYS VAL GLN ASN THR PRO GLY SEQRES 7 A 180 ALA GLU PHE VAL VAL ASP LEU PRO GLU ASP ALA VAL ILE SEQRES 8 A 180 ILE SER LYS ALA THR GLU PRO ASP LYS GLU ALA TYR SER SEQRES 9 A 180 GLY PHE GLU GLY THR ASP LEU ALA LYS ILE LEU ARG GLY SEQRES 10 A 180 ASN GLY VAL LYS ARG VAL TYR ILE CYS GLY VAL ALA THR SEQRES 11 A 180 GLU TYR CYS VAL ARG ALA THR ALA LEU ASP ALA LEU LYS SEQRES 12 A 180 HIS GLY PHE GLU VAL TYR LEU LEU ARG ASP ALA VAL LYS SEQRES 13 A 180 GLY ILE LYS PRO GLU ASP GLU GLU ARG ALA LEU GLU GLU SEQRES 14 A 180 MET LYS SER ARG GLY ILE LYS ILE VAL GLN PHE HET ZN A 400 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *128(H2 O) HELIX 1 1 ARG A 13 MET A 16 5 4 HELIX 2 2 GLU A 25 LYS A 28 5 4 HELIX 3 3 ILE A 29 LYS A 43 1 15 HELIX 4 4 ARG A 62 GLY A 65 5 4 HELIX 5 5 THR A 76 GLU A 80 5 5 HELIX 6 6 ASP A 110 ASN A 118 1 9 HELIX 7 7 TYR A 132 HIS A 144 1 13 HELIX 8 8 LYS A 159 ARG A 173 1 15 SHEET 1 A 6 VAL A 90 LYS A 94 0 SHEET 2 A 6 LEU A 46 ASP A 52 1 O ILE A 47 N VAL A 90 SHEET 3 A 6 GLU A 4 VAL A 9 1 O GLU A 4 N LEU A 46 SHEET 4 A 6 ARG A 122 VAL A 128 1 O ARG A 122 N ALA A 5 SHEET 5 A 6 GLU A 147 LYS A 156 1 O GLU A 147 N VAL A 123 SHEET 6 A 6 LYS A 176 VAL A 178 1 O LYS A 176 N LEU A 150 LINK OD2 ASP A 52 ZN ZN A 400 1555 1555 1.97 LINK NE2 HIS A 54 ZN ZN A 400 1555 1555 2.10 LINK NE2 HIS A 71 ZN ZN A 400 1555 1555 2.18 LINK O HOH A 203 ZN ZN A 400 1555 1555 2.14 LINK O HOH A 214 ZN ZN A 400 1555 1555 2.18 LINK O HOH A 223 ZN ZN A 400 1555 1555 2.37 CISPEP 1 VAL A 128 ALA A 129 0 -15.31 SITE 1 AC1 6 ASP A 52 HIS A 54 HIS A 71 HOH A 203 SITE 2 AC1 6 HOH A 214 HOH A 223 CRYST1 32.978 43.266 55.553 90.00 101.34 90.00 P 1 21 1 2 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 0.030323 0.000000 0.006081 0.00000 SCALE2 0.000000 0.023113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018359 0.00000