HEADER STRUCTURAL GENOMICS,UNKNOWN FUNCTION 18-MAR-04 1SQE TITLE 1.5A CRYSTAL STRUCTURE OF THE PROTEIN PG130 FROM STAPHYLOCOCCUS TITLE 2 AUREUS, STRUCTURAL GENOMICS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN PG130; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: MU50; 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: PDM68 KEYWDS STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, MIDWEST KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, MCSG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHANG,R.WU,G.JOACHIMIAK,O.SCHNEEWIND,A.JOACHIMIAK,MIDWEST CENTER AUTHOR 2 FOR STRUCTURAL GENOMICS (MCSG) REVDAT 5 14-FEB-24 1SQE 1 SEQADV REVDAT 4 24-FEB-09 1SQE 1 VERSN REVDAT 3 19-APR-05 1SQE 1 JRNL REVDAT 2 18-JAN-05 1SQE 1 AUTHOR KEYWDS REMARK REVDAT 1 03-AUG-04 1SQE 0 JRNL AUTH R.WU,E.P.SKAAR,R.ZHANG,G.JOACHIMIAK,P.GORNICKI,O.SCHNEEWIND, JRNL AUTH 2 A.JOACHIMIAK JRNL TITL STAPHYLOCOCCUS AUREUS ISDG AND ISDI, HEME-DEGRADING ENZYMES JRNL TITL 2 WITH STRUCTURAL SIMILARITY TO MONOOXYGENASES JRNL REF J.BIOL.CHEM. V. 280 2840 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15520015 JRNL DOI 10.1074/JBC.M409526200 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 360920.520 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 59383 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) : 0.203 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2922 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7524 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 386 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1731 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : -1.81000 REMARK 3 B33 (A**2) : 1.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.31000 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) : 0.19 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.640 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 46.23 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FRIEDEL PAIRS WERE USED IN DETERMINING REMARK 3 THIS STRUCTURE REMARK 4 REMARK 4 1SQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000021915. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795, 0.9798, 0.94656 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SBCCOLLECT REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59383 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 4.780 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: FRIEDEL PAIRS WERE USED IN DETERMINING REMARK 200 THIS STRUCTURE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, 0.25M NACL, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 19.00650 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: THIS PROTEIN EXISTED AS DIMER. MOLA AND MOLB REPRESENTS THE REMARK 300 DIMER IN ASYMMETRIC UNIT. 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: 3030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 LYS A 93 REMARK 465 ASN A 94 REMARK 465 VAL A 95 REMARK 465 ARG A 96 REMARK 465 LEU A 97 REMARK 465 LYS A 98 REMARK 465 SER A 99 REMARK 465 ASP A 100 REMARK 465 HIS B 92 REMARK 465 LYS B 93 REMARK 465 ASN B 94 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 91 -167.73 -65.73 REMARK 500 GLN B 51 -51.09 -122.14 REMARK 500 GLU B 62 -70.11 -98.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC006 RELATED DB: TARGETDB DBREF 1SQE A 17 124 UNP Q99X56 Q99X56_STAAM 1 108 DBREF 1SQE B 17 124 UNP Q99X56 Q99X56_STAAM 1 108 SEQADV 1SQE HIS A 16 UNP Q99X56 CLONING ARTIFACT SEQADV 1SQE HIS B 16 UNP Q99X56 CLONING ARTIFACT SEQRES 1 A 109 HIS MET PHE MET ALA GLU ASN ARG LEU GLN LEU GLN LYS SEQRES 2 A 109 GLY SER ALA GLU GLU THR ILE GLU ARG PHE TYR ASN ARG SEQRES 3 A 109 GLN GLY ILE GLU THR ILE GLU GLY PHE GLN GLN MET PHE SEQRES 4 A 109 VAL THR LYS THR LEU ASN THR GLU ASP THR ASP GLU VAL SEQRES 5 A 109 LYS ILE LEU THR ILE TRP GLU SER GLU ASP SER PHE ASN SEQRES 6 A 109 ASN TRP LEU ASN SER ASP VAL PHE LYS GLU ALA HIS LYS SEQRES 7 A 109 ASN VAL ARG LEU LYS SER ASP ASP ASP GLY GLN GLN SER SEQRES 8 A 109 PRO ILE LEU SER ASN LYS VAL PHE LYS TYR ASP ILE GLY SEQRES 9 A 109 TYR HIS TYR GLN LYS SEQRES 1 B 109 HIS MET PHE MET ALA GLU ASN ARG LEU GLN LEU GLN LYS SEQRES 2 B 109 GLY SER ALA GLU GLU THR ILE GLU ARG PHE TYR ASN ARG SEQRES 3 B 109 GLN GLY ILE GLU THR ILE GLU GLY PHE GLN GLN MET PHE SEQRES 4 B 109 VAL THR LYS THR LEU ASN THR GLU ASP THR ASP GLU VAL SEQRES 5 B 109 LYS ILE LEU THR ILE TRP GLU SER GLU ASP SER PHE ASN SEQRES 6 B 109 ASN TRP LEU ASN SER ASP VAL PHE LYS GLU ALA HIS LYS SEQRES 7 B 109 ASN VAL ARG LEU LYS SER ASP ASP ASP GLY GLN GLN SER SEQRES 8 B 109 PRO ILE LEU SER ASN LYS VAL PHE LYS TYR ASP ILE GLY SEQRES 9 B 109 TYR HIS TYR GLN LYS FORMUL 3 HOH *231(H2 O) HELIX 1 1 SER A 30 ILE A 35 1 6 HELIX 2 2 GLU A 36 ASN A 40 5 5 HELIX 3 3 GLY A 43 ILE A 47 5 5 HELIX 4 4 SER A 75 ASN A 84 1 10 HELIX 5 5 SER A 85 ALA A 91 1 7 HELIX 6 6 SER B 30 ARG B 37 1 8 HELIX 7 7 GLY B 43 ILE B 47 5 5 HELIX 8 8 SER B 75 ASN B 84 1 10 HELIX 9 9 SER B 85 GLU B 90 1 6 SHEET 1 A 9 PHE A 18 LEU A 26 0 SHEET 2 A 9 ASP A 65 TRP A 73 -1 O VAL A 67 N LEU A 24 SHEET 3 A 9 PHE A 50 THR A 58 -1 N GLN A 52 O ILE A 72 SHEET 4 A 9 ILE B 108 GLN B 123 -1 O ASP B 117 N LYS A 57 SHEET 5 A 9 PHE B 18 GLN B 27 -1 N ARG B 23 O LYS B 112 SHEET 6 A 9 THR B 64 TRP B 73 -1 O TRP B 73 N PHE B 18 SHEET 7 A 9 PHE B 50 THR B 58 -1 N PHE B 54 O LEU B 70 SHEET 8 A 9 ILE A 108 GLN A 123 -1 N TYR A 120 O VAL B 55 SHEET 9 A 9 PHE A 18 LEU A 26 -1 N GLN A 25 O LEU A 109 CRYST1 45.233 38.013 61.552 90.00 93.91 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 0.022108 0.000000 0.001510 0.00000 SCALE2 0.000000 0.026307 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016284 0.00000