HEADER HYDROLASE 08-MAY-01 1ILW TITLE CRYSTAL STRUCTURE OF PYRAZINAMIDASE/NICOTINAMIDASE OF PYROCOCCUS TITLE 2 HORIKOSHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: 180 AA 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834(DE3)/SJS1244; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS PYRAZINAMIDE, PYRAZINAMIDASE, NICOTINAMIDASE, TUBERCULOSIS, KEYWDS 2 HYDROLASE, CYSTEINE HYDROLASE, AMIDASE, STRUCTURAL GENOMICS, BSGC KEYWDS 3 STRUCTURE FUNDED BY NIH, PROTEIN STRUCTURE INITIATIVE, PSI, BERKELEY KEYWDS 4 STRUCTURAL GENOMICS CENTER EXPDTA X-RAY DIFFRACTION AUTHOR X.DU,S.-H.KIM,BERKELEY STRUCTURAL GENOMICS CENTER (BSGC) REVDAT 6 03-APR-24 1ILW 1 REMARK REVDAT 5 07-FEB-24 1ILW 1 REMARK REVDAT 4 24-FEB-09 1ILW 1 VERSN REVDAT 3 25-JAN-05 1ILW 1 AUTHOR KEYWDS REMARK REVDAT 2 24-AUG-04 1ILW 1 KEYWDS REVDAT 1 12-DEC-01 1ILW 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. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.189 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.181 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 954 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 9837 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL 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)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1412 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH $ HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ILW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000013396. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-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 : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9862 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.246 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.11800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 17.40 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: A STRUCTURE OF THE SAME PROTEIN OBTAINED ON MAD REMARK 200 DATA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22.5% PEG3350, 250 MM AMMONIUM REMARK 280 ACETATE, 100 MM SODIUM ACETATE, PH 4.6. SEEDING., VAPOR REMARK 280 DIFFUSION, 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 21.70900 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 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 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 PHE A 180 C PHE A 180 O 0.219 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 ALA A 102 101.60 -166.06 REMARK 500 TYR A 132 -96.73 -117.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BSGCAIR30510 RELATED DB: TARGETDB DBREF 1ILW 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 FORMUL 2 HOH *88(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 GLY A 174 1 16 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 CISPEP 1 VAL A 128 ALA A 129 0 -14.28 CRYST1 32.977 43.418 55.781 90.00 101.22 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 0.030324 0.000000 0.006014 0.00000 SCALE2 0.000000 0.023032 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018276 0.00000