HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 06-JUL-06 2DST TITLE CRYSTAL STRUCTURE ANALYSIS OF TT1977 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN TTHA1544; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS CONSERVED HYPOTHETICAL PROTEIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 2 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIE,S.KISHISHITA,K.MURAYAMA,M.SHIROUZU,L.CHEN,Z.J.LIU,B.C.WANG, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 13-MAR-24 2DST 1 REMARK REVDAT 4 09-JUN-09 2DST 1 REVDAT REVDAT 3 24-FEB-09 2DST 1 VERSN REVDAT 2 27-JAN-09 2DST 1 JRNL REVDAT 1 06-JAN-07 2DST 0 JRNL AUTH Y.XIE,C.TAKEMOTO,S.KISHISHITA,T.UCHIKUBO-KAMO,K.MURAYAMA, JRNL AUTH 2 L.CHEN,Z.J.LIU,B.C.WANG,M.MANZOKU,A.EBIHARA,S.KURAMITSU, JRNL AUTH 3 M.SHIROUZU,S.YOKOYAMA JRNL TITL STRUCTURE OF THE MINIMIZED ALPHA/BETA-HYDROLASE FOLD PROTEIN JRNL TITL 2 FROM THERMUS THERMOPHILUS HB8. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 63 993 2007 JRNL REFN ESSN 1744-3091 JRNL PMID 18084077 JRNL DOI 10.1107/S1744309107061106 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 741938.110 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 82.5 REMARK 3 NUMBER OF REFLECTIONS : 13671 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) : 0.201 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1325 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) (%) : 58.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1467 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 156 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1858 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 146 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.81000 REMARK 3 B22 (A**2) : 24.44000 REMARK 3 B33 (A**2) : -16.63000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.95000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.35 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 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) : 1.420 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.280 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.010 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 63.80 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 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DST COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000025802. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-06; 16-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; APS REMARK 200 BEAMLINE : BL26B1; 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000; 0.9724 REMARK 200 MONOCHROMATOR : SILICON; SILICON REMARK 200 OPTICS : MIRRORS; MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210; MARMOSAIC REMARK 200 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15276 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.4360 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.15100 REMARK 200 R SYM FOR SHELL (I) : 0.15100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.640 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 43.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M 1,6-HEXANEDIOL, 0.1M NA ACETATE (PH REMARK 280 4.6), 0.005M COCL2, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 32.91100 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: IN THIS CRYSTAL PACKING, IT LOOKS LIKE DIMER. BUT, THERE IS REMARK 300 NO EXPERIMENTAL EVIDENCE. 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 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 MET A 1 REMARK 465 ASN A 124 REMARK 465 ILE A 125 REMARK 465 ASP A 126 REMARK 465 LEU A 127 REMARK 465 GLY A 128 REMARK 465 GLY A 129 REMARK 465 ASN A 130 REMARK 465 LEU A 131 REMARK 465 MET B 1 REMARK 465 ASN B 124 REMARK 465 ILE B 125 REMARK 465 ASP B 126 REMARK 465 LEU B 127 REMARK 465 GLY B 128 REMARK 465 GLY B 129 REMARK 465 ASN B 130 REMARK 465 LEU B 131 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 VAL B 19 144.49 -177.67 REMARK 500 LEU B 120 -62.88 171.21 REMARK 500 TYR B 122 70.00 9.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CYD RELATED DB: PDB REMARK 900 31% AMINO ACID IDENTITY WITH THAT OF TT1977 REMARK 900 RELATED ID: TTK003001977.1 RELATED DB: TARGETDB DBREF 2DST A 1 131 UNP Q5SI36 Q5SI36_THET8 1 131 DBREF 2DST B 1 131 UNP Q5SI36 Q5SI36_THET8 1 131 SEQRES 1 A 131 MET ARG ARG ALA GLY TYR LEU HIS LEU TYR GLY LEU ASN SEQRES 2 A 131 LEU VAL PHE ASP ARG VAL GLY LYS GLY PRO PRO VAL LEU SEQRES 3 A 131 LEU VAL ALA GLU GLU ALA SER ARG TRP PRO GLU ALA LEU SEQRES 4 A 131 PRO GLU GLY TYR ALA PHE TYR LEU LEU ASP LEU PRO GLY SEQRES 5 A 131 TYR GLY ARG THR GLU GLY PRO ARG MET ALA PRO GLU GLU SEQRES 6 A 131 LEU ALA HIS PHE VAL ALA GLY PHE ALA VAL MET MET ASN SEQRES 7 A 131 LEU GLY ALA PRO TRP VAL LEU LEU ARG GLY LEU GLY LEU SEQRES 8 A 131 ALA LEU GLY PRO HIS LEU GLU ALA LEU GLY LEU ARG ALA SEQRES 9 A 131 LEU PRO ALA GLU GLY VAL GLU VAL ALA GLU VAL LEU SER SEQRES 10 A 131 SER LYS LEU SER TYR GLY ASN ILE ASP LEU GLY GLY ASN SEQRES 11 A 131 LEU SEQRES 1 B 131 MET ARG ARG ALA GLY TYR LEU HIS LEU TYR GLY LEU ASN SEQRES 2 B 131 LEU VAL PHE ASP ARG VAL GLY LYS GLY PRO PRO VAL LEU SEQRES 3 B 131 LEU VAL ALA GLU GLU ALA SER ARG TRP PRO GLU ALA LEU SEQRES 4 B 131 PRO GLU GLY TYR ALA PHE TYR LEU LEU ASP LEU PRO GLY SEQRES 5 B 131 TYR GLY ARG THR GLU GLY PRO ARG MET ALA PRO GLU GLU SEQRES 6 B 131 LEU ALA HIS PHE VAL ALA GLY PHE ALA VAL MET MET ASN SEQRES 7 B 131 LEU GLY ALA PRO TRP VAL LEU LEU ARG GLY LEU GLY LEU SEQRES 8 B 131 ALA LEU GLY PRO HIS LEU GLU ALA LEU GLY LEU ARG ALA SEQRES 9 B 131 LEU PRO ALA GLU GLY VAL GLU VAL ALA GLU VAL LEU SER SEQRES 10 B 131 SER LYS LEU SER TYR GLY ASN ILE ASP LEU GLY GLY ASN SEQRES 11 B 131 LEU FORMUL 3 HOH *146(H2 O) HELIX 1 1 GLU A 31 TRP A 35 5 5 HELIX 2 2 ALA A 62 MET A 77 1 16 HELIX 3 3 GLY A 88 ALA A 92 5 5 HELIX 4 4 LEU A 93 LEU A 100 1 8 HELIX 5 5 GLU A 111 TYR A 122 1 12 HELIX 6 6 GLU B 31 TRP B 35 5 5 HELIX 7 7 ALA B 62 MET B 77 1 16 HELIX 8 8 GLY B 88 ALA B 92 5 5 HELIX 9 9 LEU B 93 LEU B 100 1 8 HELIX 10 10 GLU B 111 LYS B 119 1 9 SHEET 1 A 6 ARG A 3 LEU A 9 0 SHEET 2 A 6 LEU A 12 VAL A 19 -1 O LEU A 12 N LEU A 9 SHEET 3 A 6 ALA A 44 ASP A 49 -1 O LEU A 47 N ASP A 17 SHEET 4 A 6 PRO A 24 ALA A 29 1 N VAL A 25 O ALA A 44 SHEET 5 A 6 TRP A 83 LEU A 86 1 O LEU A 85 N VAL A 28 SHEET 6 A 6 ALA A 104 PRO A 106 1 O LEU A 105 N VAL A 84 SHEET 1 B 6 ARG B 3 LEU B 9 0 SHEET 2 B 6 LEU B 12 VAL B 19 -1 O LEU B 12 N LEU B 9 SHEET 3 B 6 ALA B 44 LEU B 48 -1 O LEU B 47 N ASP B 17 SHEET 4 B 6 PRO B 24 VAL B 28 1 N LEU B 27 O TYR B 46 SHEET 5 B 6 TRP B 83 LEU B 86 1 O LEU B 85 N VAL B 28 SHEET 6 B 6 ALA B 104 PRO B 106 1 O LEU B 105 N VAL B 84 CRYST1 31.714 65.822 59.320 90.00 92.61 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 0.031532 0.000000 0.001437 0.00000 SCALE2 0.000000 0.015192 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016875 0.00000