HEADER OXIDOREDUCTASE 22-AUG-03 1Q98 TITLE STRUCTURE OF A THIOL PEROXIDASE FROM HAEMOPHILUS INFLUENZAE RD COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL PEROXIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TPX; COMPND 5 EC: 1.11.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 GENE: TPX, HI0751; 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: PET T7; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS STRUCTURAL GENOMICS, TPX, PEROXIDASE, NYSGXRC, T1429, PSI, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.KNIEWEL,J.BUGLINO,V.SOLORZANO,J.WU,C.D.LIMA,S.K.BURLEY,NEW YORK SGX AUTHOR 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 4 03-FEB-21 1Q98 1 AUTHOR REVDAT 3 24-FEB-09 1Q98 1 VERSN REVDAT 2 25-JAN-05 1Q98 1 AUTHOR KEYWDS REMARK REVDAT 1 09-SEP-03 1Q98 0 JRNL AUTH R.KNIEWEL,J.BUGLINO,V.SOLORZANO,J.WU,C.D.LIMA JRNL TITL STRUCTURE OF A THIOL PEROXIDASE FROM HAEMOPHILUS INFLUENZAE JRNL TITL 2 RD JRNL REF TO BE PUBLISHED JRNL REFN 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 23960 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) : 0.225 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1203 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) (%) : 93.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3654 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 194 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2464 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.91000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : -5.60000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -9.31000 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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) : 1.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.400 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.050 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.010 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 62.80 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1Q98 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000020075. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 24220 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.16200 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: SIRAS ON HG REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19-24% PEGV 4000, 0.1M AMMONIUM REMARK 280 ACETATE, 0.1M SODIUM ACETATE PH 4.5, 5%ETHYLENE GLYCOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 21.83350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 465 MET B 1 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 GLN A 89 -7.94 -58.06 REMARK 500 ASN A 100 40.95 -96.81 REMARK 500 ALA B 60 -146.16 -79.93 REMARK 500 THR B 61 -53.17 -163.01 REMARK 500 ALA B 95 41.17 -149.83 REMARK 500 GLU B 96 -88.18 -69.02 REMARK 500 ASN B 100 24.53 -77.09 REMARK 500 ASN B 109 51.97 -153.79 REMARK 500 LYS B 152 31.23 -80.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T1429 RELATED DB: TARGETDB DBREF 1Q98 A 1 165 UNP Q57549 TPX_HAEIN 1 165 DBREF 1Q98 B 1 165 UNP Q57549 TPX_HAEIN 1 165 SEQRES 1 A 165 MET THR VAL THR LEU ALA GLY ASN PRO ILE GLU VAL GLY SEQRES 2 A 165 GLY HIS PHE PRO GLN VAL GLY GLU ILE VAL GLU ASN PHE SEQRES 3 A 165 ILE LEU VAL GLY ASN ASP LEU ALA ASP VAL ALA LEU ASN SEQRES 4 A 165 ASP PHE ALA SER LYS ARG LYS VAL LEU ASN ILE PHE PRO SEQRES 5 A 165 SER ILE ASP THR GLY VAL CYS ALA THR SER VAL ARG LYS SEQRES 6 A 165 PHE ASN GLN GLN ALA ALA LYS LEU SER ASN THR ILE VAL SEQRES 7 A 165 LEU CYS ILE SER ALA ASP LEU PRO PHE ALA GLN ALA ARG SEQRES 8 A 165 PHE CYS GLY ALA GLU GLY ILE GLU ASN ALA LYS THR VAL SEQRES 9 A 165 SER THR PHE ARG ASN HIS ALA LEU HIS SER GLN LEU GLY SEQRES 10 A 165 VAL ASP ILE GLN THR GLY PRO LEU ALA GLY LEU THR SER SEQRES 11 A 165 ARG ALA VAL ILE VAL LEU ASP GLU GLN ASN ASN VAL LEU SEQRES 12 A 165 HIS SER GLN LEU VAL GLU GLU ILE LYS GLU GLU PRO ASN SEQRES 13 A 165 TYR GLU ALA ALA LEU ALA VAL LEU ALA SEQRES 1 B 165 MET THR VAL THR LEU ALA GLY ASN PRO ILE GLU VAL GLY SEQRES 2 B 165 GLY HIS PHE PRO GLN VAL GLY GLU ILE VAL GLU ASN PHE SEQRES 3 B 165 ILE LEU VAL GLY ASN ASP LEU ALA ASP VAL ALA LEU ASN SEQRES 4 B 165 ASP PHE ALA SER LYS ARG LYS VAL LEU ASN ILE PHE PRO SEQRES 5 B 165 SER ILE ASP THR GLY VAL CYS ALA THR SER VAL ARG LYS SEQRES 6 B 165 PHE ASN GLN GLN ALA ALA LYS LEU SER ASN THR ILE VAL SEQRES 7 B 165 LEU CYS ILE SER ALA ASP LEU PRO PHE ALA GLN ALA ARG SEQRES 8 B 165 PHE CYS GLY ALA GLU GLY ILE GLU ASN ALA LYS THR VAL SEQRES 9 B 165 SER THR PHE ARG ASN HIS ALA LEU HIS SER GLN LEU GLY SEQRES 10 B 165 VAL ASP ILE GLN THR GLY PRO LEU ALA GLY LEU THR SER SEQRES 11 B 165 ARG ALA VAL ILE VAL LEU ASP GLU GLN ASN ASN VAL LEU SEQRES 12 B 165 HIS SER GLN LEU VAL GLU GLU ILE LYS GLU GLU PRO ASN SEQRES 13 B 165 TYR GLU ALA ALA LEU ALA VAL LEU ALA FORMUL 3 HOH *275(H2 O) HELIX 1 1 ASN A 39 ALA A 42 5 4 HELIX 2 2 ALA A 60 LEU A 73 1 14 HELIX 3 3 LEU A 85 ALA A 90 1 6 HELIX 4 4 HIS A 110 LEU A 116 1 7 HELIX 5 5 ASN A 156 VAL A 163 1 8 HELIX 6 6 ASN B 39 ALA B 42 5 4 HELIX 7 7 THR B 61 LYS B 72 1 12 HELIX 8 8 LEU B 85 ALA B 90 1 6 HELIX 9 9 HIS B 110 LEU B 116 1 7 HELIX 10 10 ASN B 156 ALA B 165 1 10 SHEET 1 A 2 VAL A 3 LEU A 5 0 SHEET 2 A 2 ASN A 8 ILE A 10 -1 O ASN A 8 N LEU A 5 SHEET 1 B 2 VAL A 12 GLY A 13 0 SHEET 2 B 2 ASP A 119 ILE A 120 -1 O ASP A 119 N GLY A 13 SHEET 1 C 2 ILE A 27 VAL A 29 0 SHEET 2 C 2 ASP A 35 ALA A 37 -1 O VAL A 36 N LEU A 28 SHEET 1 D 5 ALA A 101 SER A 105 0 SHEET 2 D 5 THR A 76 SER A 82 1 N CYS A 80 O LYS A 102 SHEET 3 D 5 ARG A 45 ILE A 50 1 N VAL A 47 O LEU A 79 SHEET 4 D 5 ALA A 132 LEU A 136 -1 O ILE A 134 N LEU A 48 SHEET 5 D 5 VAL A 142 LEU A 147 -1 O LEU A 143 N VAL A 135 SHEET 1 E 2 VAL B 3 LEU B 5 0 SHEET 2 E 2 ASN B 8 ILE B 10 -1 O ASN B 8 N LEU B 5 SHEET 1 F 2 VAL B 12 GLY B 13 0 SHEET 2 F 2 ASP B 119 ILE B 120 -1 O ASP B 119 N GLY B 13 SHEET 1 G 2 ILE B 27 VAL B 29 0 SHEET 2 G 2 ASP B 35 ALA B 37 -1 O VAL B 36 N LEU B 28 SHEET 1 H 5 ALA B 101 SER B 105 0 SHEET 2 H 5 THR B 76 SER B 82 1 N CYS B 80 O LYS B 102 SHEET 3 H 5 ARG B 45 ILE B 50 1 N VAL B 47 O LEU B 79 SHEET 4 H 5 ALA B 132 LEU B 136 -1 O ILE B 134 N LEU B 48 SHEET 5 H 5 VAL B 142 LEU B 147 -1 O HIS B 144 N VAL B 135 SSBOND 1 CYS A 59 CYS A 93 1555 1555 2.03 SSBOND 2 CYS B 59 CYS B 93 1555 1555 2.03 CRYST1 35.033 43.667 104.587 90.00 97.34 90.00 P 1 21 1 4 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 0.028545 0.000000 0.003677 0.00000 SCALE2 0.000000 0.022901 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009640 0.00000