HEADER BIOSYNTHETIC PROTEIN 29-JUN-07 2QGO TITLE CRYSTAL STRUCTURE OF A PUTATIVE FE-S BIOSYNTHESIS PROTEIN FROM TITLE 2 LACTOBACILLUS ACIDOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE FE-S BIOSYNTHESIS PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS ACIDOPHILUS; SOURCE 3 ORGANISM_TAXID: 272621; SOURCE 4 STRAIN: NCFM; SOURCE 5 GENE: LBA0486; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODON+RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSGX3(BC) KEYWDS PSI-2, NYSGXRC, 10399G, FE-S CLUSTER PROTEIN, STRUCTURAL GENOMICS, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.AGARWAL,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 5 21-FEB-24 2QGO 1 REMARK REVDAT 4 03-FEB-21 2QGO 1 AUTHOR JRNL SEQADV REVDAT 3 13-JUL-11 2QGO 1 VERSN REVDAT 2 24-FEB-09 2QGO 1 VERSN REVDAT 1 31-JUL-07 2QGO 0 JRNL AUTH R.AGARWAL,S.K.BURLEY,S.SWAMINATHAN JRNL TITL STRUCTURAL ANALYSIS OF FE-S CLUSTER PROTEINS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.04 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 75670.770 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 17469 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) : 0.226 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 512 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2140 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 62 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.042 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 886 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.94000 REMARK 3 B22 (A**2) : 1.94000 REMARK 3 B33 (A**2) : -3.87000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 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 : 42.57 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.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: THE FRIEDEL PAIRS WERE USED FOR REMARK 3 PHASING. RESIDUES LISTED AS MISSING IN REMARK 465 ARE DUE TO REMARK 3 LACK OF ELECTRON DENSITY. RESIDUES WITH MISSING ATOMS LISTED IN REMARK 3 REMARK 470 ARE DUE TO LACK OF ELECTRON DENSITY FOR SIDE CHAINS REMARK 3 AND MODELED AS ALANINES. REMARK 4 REMARK 4 2QGO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000043575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : SI(III) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17922 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.21300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM CITRATE, PH 7.0, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.22100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.11050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.33150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 465 SER A 2 REMARK 465 LEU A 3 REMARK 465 GLN A 40 REMARK 465 GLY A 41 REMARK 465 GLY A 42 REMARK 465 SER A 43 REMARK 465 CYS A 44 REMARK 465 SER A 45 REMARK 465 MET A 46 REMARK 465 GLY A 47 REMARK 465 ALA A 48 REMARK 465 MET A 127 REMARK 465 GLY A 128 REMARK 465 ILE A 129 REMARK 465 ASN A 130 REMARK 465 ARG A 131 REMARK 465 GLN A 132 REMARK 465 CYS A 133 REMARK 465 GLU A 134 REMARK 465 GLY A 135 REMARK 465 HIS A 136 REMARK 465 HIS A 137 REMARK 465 HIS A 138 REMARK 465 HIS A 139 REMARK 465 HIS A 140 REMARK 465 HIS A 141 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-10399G RELATED DB: TARGETDB DBREF 2QGO A 4 133 UNP Q5FLQ3 Q5FLQ3_LACAC 2 131 SEQADV 2QGO MET A 1 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO SER A 2 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO LEU A 3 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO GLU A 134 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO GLY A 135 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO HIS A 136 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO HIS A 137 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO HIS A 138 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO HIS A 139 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO HIS A 140 UNP Q5FLQ3 CLONING ARTIFACT SEQADV 2QGO HIS A 141 UNP Q5FLQ3 CLONING ARTIFACT SEQRES 1 A 141 MET SER LEU LEU ASN ILE LYS PHE THR ASP ASN ALA VAL SEQRES 2 A 141 ASP TYR LEU LYS ARG ARG GLU ILE LEU ASP LYS ILE LEU SEQRES 3 A 141 ILE LEU ILE THR ASP ASP GLY GLY GLY LYS TYR SER ILE SEQRES 4 A 141 GLN GLY GLY SER CYS SER MET GLY ALA HIS PHE SER ILE SEQRES 5 A 141 ILE TRP LEU ASP LYS VAL ASP PRO ASP TYR PRO VAL LYS SEQRES 6 A 141 ILE ALA ASN GLU GLN ASN VAL LYS ILE TYR THR SER ASP SEQRES 7 A 141 PHE ASP LYS THR MET LEU GLY PRO ASN MET VAL MET ASP SEQRES 8 A 141 TYR ASN ALA GLY SER LEU SER LEU SER SER ASP GLU GLY SEQRES 9 A 141 LEU LEU ASP GLY SER VAL ASP ILE GLY ASN GLY ALA ALA SEQRES 10 A 141 LEU LEU LYS ALA ASN LYS ASN VAL GLN MET GLY ILE ASN SEQRES 11 A 141 ARG GLN CYS GLU GLY HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *29(H2 O) HELIX 1 1 THR A 9 ARG A 19 1 11 HELIX 2 2 SER A 77 THR A 82 1 6 HELIX 3 3 GLY A 115 GLN A 126 1 12 SHEET 1 A 8 ILE A 6 PHE A 8 0 SHEET 2 A 8 MET A 88 ASN A 93 1 O MET A 90 N LYS A 7 SHEET 3 A 8 SER A 96 SER A 101 -1 O SER A 98 N ASP A 91 SHEET 4 A 8 GLY A 104 ASN A 114 -1 O ASP A 107 N LEU A 99 SHEET 5 A 8 PHE A 50 LEU A 55 1 N ILE A 52 O ASP A 111 SHEET 6 A 8 ILE A 25 THR A 30 -1 N ILE A 27 O ILE A 53 SHEET 7 A 8 LYS A 73 THR A 76 1 O LYS A 73 N LEU A 26 SHEET 8 A 8 VAL A 64 LYS A 65 -1 N VAL A 64 O THR A 76 CRYST1 61.261 61.261 40.442 90.00 90.00 90.00 P 41 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 0.016324 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024727 0.00000