HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 05-DEC-03 1V70 TITLE CRYSTAL STRUCTURE OF PROBABLE ANTIBIOTICS SYNTHESIS PROTEIN FROM TITLE 2 THERMUS THERMOPHILUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ANTIBIOTICS SYNTHESIS PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; 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: PET11A KEYWDS STRUCTURAL GENOMICS, THERMUS THERMOPHILUS HB8, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.ASADA,N.KUNISHIMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 2 (RSGI) REVDAT 4 27-DEC-23 1V70 1 REMARK LINK REVDAT 3 13-JUL-11 1V70 1 VERSN REVDAT 2 24-FEB-09 1V70 1 VERSN REVDAT 1 14-DEC-04 1V70 0 JRNL AUTH Y.ASADA,N.KUNISHIMA JRNL TITL CRYSTAL STRUCTURE OF PROBABLE ANTIBIOTICS SYNTHESIS PROTEIN JRNL TITL 2 FROM THERMUS THERMOPHILUS HB8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.57 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) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 32473 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 : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1592 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.36 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 188 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 : 808 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.11000 REMARK 3 B22 (A**2) : 2.11000 REMARK 3 B33 (A**2) : -4.22000 REMARK 3 B12 (A**2) : 0.72000 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) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1V70 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000006285. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-03; NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0; NULL REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; NULL REMARK 200 RADIATION SOURCE : SPRING-8; NULL REMARK 200 BEAMLINE : BL26B1; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0, 0.97954; NULL REMARK 200 MONOCHROMATOR : BENDING MAGNET; NULL REMARK 200 OPTICS : MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; NULL REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32494 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.63200 REMARK 200 R SYM FOR SHELL (I) : 0.58200 REMARK 200 FOR SHELL : 3.620 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD WITH DATA COLLECTION REMARK 200 ON SE-MET CRYSTAL AT 0.97954 A REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, HEPES, PH 7.1, REMARK 280 MICROBATCH, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.66167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.32333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.32333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.66167 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: THE BIOLOGICAL ASSEMBLY IS DIMER GENERATED FROM THE MONOMER REMARK 300 IN THE ASYMMETRIC UNIT BY THE OPERATION: Y,X,-Z 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1092 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 26 CD OE1 OE2 REMARK 480 GLU A 47 CD OE1 OE2 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1001 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 22 O REMARK 620 2 HOH A1035 O 83.1 REMARK 620 3 HOH A1055 O 95.1 78.4 REMARK 620 4 HOH A1081 O 165.2 82.7 86.4 REMARK 620 5 HOH A1085 O 108.1 151.4 74.5 86.6 REMARK 620 6 HOH A1123 O 92.1 121.0 160.1 91.4 85.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003001209.1 RELATED DB: TARGETDB DBREF 1V70 A 1 105 UNP Q5SM39 Q5SM39_THET8 1 105 SEQRES 1 A 105 MET GLU ILE LYS ASP LEU LYS ARG LEU ALA ARG TYR ASN SEQRES 2 A 105 PRO GLU LYS MET ALA LYS ILE PRO VAL PHE GLN SER GLU SEQRES 3 A 105 ARG MET LEU TYR ASP LEU TYR ALA LEU LEU PRO GLY GLN SEQRES 4 A 105 ALA GLN LYS VAL HIS VAL HIS GLU GLY SER ASP LYS VAL SEQRES 5 A 105 TYR TYR ALA LEU GLU GLY GLU VAL VAL VAL ARG VAL GLY SEQRES 6 A 105 GLU GLU GLU ALA LEU LEU ALA PRO GLY MET ALA ALA PHE SEQRES 7 A 105 ALA PRO ALA GLY ALA PRO HIS GLY VAL ARG ASN GLU SER SEQRES 8 A 105 ALA SER PRO ALA LEU LEU LEU VAL VAL THR ALA PRO ARG SEQRES 9 A 105 PRO HET NA A1001 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *122(H2 O) HELIX 1 1 ASP A 5 ALA A 10 1 6 SHEET 1 A 5 ALA A 18 SER A 25 0 SHEET 2 A 5 MET A 28 LEU A 35 -1 O LEU A 32 N ILE A 20 SHEET 3 A 5 ALA A 95 ALA A 102 -1 O VAL A 99 N ASP A 31 SHEET 4 A 5 ASP A 50 GLU A 57 -1 N ASP A 50 O ALA A 102 SHEET 5 A 5 ALA A 76 ALA A 79 -1 O ALA A 79 N LYS A 51 SHEET 1 B 4 ALA A 40 HIS A 44 0 SHEET 2 B 4 HIS A 85 ARG A 88 -1 O VAL A 87 N GLN A 41 SHEET 3 B 4 VAL A 60 VAL A 64 -1 N VAL A 61 O ARG A 88 SHEET 4 B 4 GLU A 67 LEU A 71 -1 O LEU A 71 N VAL A 60 LINK O VAL A 22 NA NA A1001 1555 1555 2.33 LINK NA NA A1001 O HOH A1035 1555 1555 2.63 LINK NA NA A1001 O HOH A1055 1555 1555 2.56 LINK NA NA A1001 O HOH A1081 1555 1555 2.61 LINK NA NA A1001 O HOH A1085 1555 1555 2.59 LINK NA NA A1001 O HOH A1123 1555 1555 2.46 CISPEP 1 ALA A 102 PRO A 103 0 -0.50 SITE 1 AC1 6 VAL A 22 HOH A1035 HOH A1055 HOH A1081 SITE 2 AC1 6 HOH A1085 HOH A1123 CRYST1 74.527 74.527 40.985 90.00 90.00 120.00 P 31 2 1 6 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 0.013418 0.007747 0.000000 0.00000 SCALE2 0.000000 0.015494 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024399 0.00000