HEADER GENE REGULATION 03-MAR-04 1VC1 TITLE CRYSTAL STRUCTURE OF THE TM1442 PROTEIN FROM THERMOTOGA MARITIMA, A TITLE 2 HOMOLOG OF THE BACILLUS SUBTILIS GENERAL STRESS RESPONSE ANTI-ANTI- TITLE 3 SIGMA FACTOR RSBV COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE ANTI-SIGMA FACTOR ANTAGONIST TM1442; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TM1442 PROTEIN, GENERAL STRESS RESPONSE ANTI-ANTI-SIGMA COMPND 5 FACTOR; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: TM1442; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTI-ANTI-SIGMA FACTOR, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.LEE,H.J.AHN,K.S.HA,S.W.SUH REVDAT 3 27-DEC-23 1VC1 1 REMARK REVDAT 2 24-FEB-09 1VC1 1 VERSN REVDAT 1 28-SEP-04 1VC1 0 JRNL AUTH J.Y.LEE,H.J.AHN,K.S.HA,S.W.SUH JRNL TITL CRYSTAL STRUCTURE OF THE TM1442 PROTEIN FROM THERMOTOGA JRNL TITL 2 MARITIMA, A HOMOLOG OF THE BACILLUS SUBTILIS GENERAL STRESS JRNL TITL 3 RESPONSE ANTI-ANTI-SIGMA FACTOR RSBV JRNL REF PROTEINS V. 56 176 2004 JRNL REFN ISSN 0887-3585 JRNL PMID 15162498 JRNL DOI 10.1002/PROT.20166 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 807204.180 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 12842 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) : 0.205 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1324 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1864 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE : 0.2330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 210 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1726 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.56000 REMARK 3 B22 (A**2) : -6.31000 REMARK 3 B33 (A**2) : -1.25000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.940 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 : 0.35 REMARK 3 BSOL : 68.89 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VC1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000006448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-99 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12842 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 96.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE, 100MM MAGNESIUM REMARK 280 CHLORIDE, 18%(V/V) POLYETHYLENE GLYCOL 400, PH 4.6, 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 58.41550 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: 1290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10480 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 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 ASN A 2 -135.62 -94.86 REMARK 500 ASN A 3 167.15 -49.04 REMARK 500 LEU A 4 118.08 140.80 REMARK 500 ASP A 12 -124.01 56.82 REMARK 500 ASN A 27 10.27 -145.81 REMARK 500 THR A 42 150.54 -48.28 REMARK 500 ASN B 2 -126.67 -100.13 REMARK 500 LEU B 4 97.33 140.20 REMARK 500 ASP B 12 -123.66 55.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 1VC1 A 1 110 UNP Q9X1F5 Y1442_THEMA 1 110 DBREF 1VC1 B 1 110 UNP Q9X1F5 Y1442_THEMA 1 110 SEQRES 1 A 110 MET ASN ASN LEU LYS LEU ASP ILE VAL GLU GLN ASP ASP SEQRES 2 A 110 LYS ALA ILE VAL ARG VAL GLN GLY ASP ILE ASP ALA TYR SEQRES 3 A 110 ASN SER SER GLU LEU LYS GLU GLN LEU ARG ASN PHE ILE SEQRES 4 A 110 SER THR THR SER LYS LYS LYS ILE VAL LEU ASP LEU SER SEQRES 5 A 110 SER VAL SER TYR MET ASP SER ALA GLY LEU GLY THR LEU SEQRES 6 A 110 VAL VAL ILE LEU LYS ASP ALA LYS ILE ASN GLY LYS GLU SEQRES 7 A 110 PHE ILE LEU SER SER LEU LYS GLU SER ILE SER ARG ILE SEQRES 8 A 110 LEU LYS LEU THR HIS LEU ASP LYS ILE PHE LYS ILE THR SEQRES 9 A 110 ASP THR VAL GLU GLU ALA SEQRES 1 B 110 MET ASN ASN LEU LYS LEU ASP ILE VAL GLU GLN ASP ASP SEQRES 2 B 110 LYS ALA ILE VAL ARG VAL GLN GLY ASP ILE ASP ALA TYR SEQRES 3 B 110 ASN SER SER GLU LEU LYS GLU GLN LEU ARG ASN PHE ILE SEQRES 4 B 110 SER THR THR SER LYS LYS LYS ILE VAL LEU ASP LEU SER SEQRES 5 B 110 SER VAL SER TYR MET ASP SER ALA GLY LEU GLY THR LEU SEQRES 6 B 110 VAL VAL ILE LEU LYS ASP ALA LYS ILE ASN GLY LYS GLU SEQRES 7 B 110 PHE ILE LEU SER SER LEU LYS GLU SER ILE SER ARG ILE SEQRES 8 B 110 LEU LYS LEU THR HIS LEU ASP LYS ILE PHE LYS ILE THR SEQRES 9 B 110 ASP THR VAL GLU GLU ALA FORMUL 3 HOH *177(H2 O) HELIX 1 1 ASN A 27 THR A 42 1 16 HELIX 2 2 ASP A 58 ASN A 75 1 18 HELIX 3 3 LYS A 85 THR A 95 1 11 HELIX 4 4 HIS A 96 ILE A 100 5 5 HELIX 5 5 ASN B 27 THR B 41 1 15 HELIX 6 6 ASP B 58 ASN B 75 1 18 HELIX 7 7 LYS B 85 THR B 95 1 11 HELIX 8 8 HIS B 96 ILE B 100 5 5 SHEET 1 A 5 LYS A 5 GLN A 11 0 SHEET 2 A 5 LYS A 14 GLN A 20 -1 O ILE A 16 N VAL A 9 SHEET 3 A 5 LYS A 46 SER A 53 1 O VAL A 48 N VAL A 17 SHEET 4 A 5 GLU A 78 SER A 82 1 O GLU A 78 N ILE A 47 SHEET 5 A 5 LYS A 102 THR A 104 1 O LYS A 102 N LEU A 81 SHEET 1 B 5 LYS B 5 GLN B 11 0 SHEET 2 B 5 LYS B 14 GLN B 20 -1 O ILE B 16 N VAL B 9 SHEET 3 B 5 LYS B 46 ASP B 50 1 O VAL B 48 N VAL B 17 SHEET 4 B 5 GLU B 78 SER B 82 1 O GLU B 78 N ILE B 47 SHEET 5 B 5 LYS B 102 THR B 104 1 O LYS B 102 N LEU B 81 CRYST1 31.544 116.831 31.392 90.00 119.84 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 0.031702 0.000000 0.018184 0.00000 SCALE2 0.000000 0.008559 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036724 0.00000