HEADER STRUCTURAL GENOMICS,UNKNOWN FUNCTION 18-MAR-04 1SQE TITLE 1.5A CRYSTAL STRUCTURE OF THE PROTEIN PG130 FROM TITLE 2 STAPHYLOCOCCUS 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, KEYWDS 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, STRUCTURAL KEYWDS 3 GENOMICS,UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHANG,R.WU,G.JOACHIMIAK,O.SCHNEEWIND,A.JOACHIMIAK,MIDWEST AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (MCSG) 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, JRNL AUTH 2 O.SCHNEEWIND,A.JOACHIMIAK JRNL TITL STAPHYLOCOCCUS AUREUS ISDG AND ISDI, JRNL TITL 2 HEME-DEGRADING ENZYMES WITH STRUCTURAL SIMILARITY JRNL TITL 3 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 1 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) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.64 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 REMARK 3 DETERMINING THIS STRUCTURE REMARK 4 REMARK 4 1SQE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-04. REMARK 100 THE RCSB ID CODE IS RCSB021915. 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 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 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 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 REMARK 300 THE 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 MASTER 256 0 0 9 9 0 0 6 0 0 0 18 END