PDB Short entry for 1WNA HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 28-JUL-04 1WNA TITLE CRYSTAL STRUCTURE OF THE HYPOTHETICAL PROTEIN TT1805 FROM THERMUS TITLE 2 THERMOPHILLUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THE HYPOTHETICAL PROTEIN (TT1805); 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS THERMUS THERMOPHILLUS, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.A.PIOSZAK,S.KISHISHITA,M.SHIROUZU,S.KURAMITSU,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 13-JUL-11 1WNA 1 VERSN REVDAT 2 24-FEB-09 1WNA 1 VERSN REVDAT 1 28-JAN-05 1WNA 0 JRNL AUTH A.A.PIOSZAK,S.KISHISHITA,M.SHIROUZU,S.KURAMITSU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF THE HYPOTHETICAL PROTEIN TT1805 FROM JRNL TITL 2 THERMUS THERMOPHILLUS HB8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 812070.460 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 35491 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) : 0.208 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1758 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2582 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 162 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 : 967 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.89000 REMARK 3 B22 (A**2) : 5.03000 REMARK 3 B33 (A**2) : -1.14000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.77 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) : 3.160 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.970 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.760 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.000 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 48.02 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 1WNA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUL-04. REMARK 100 THE RCSB ID CODE IS RCSB023772. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97912, 0.97944, 0.964 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36267 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 37.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.614 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5556 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.529 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 52.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 8000, 20% GLYCEROL, 40MM REMARK 280 POTASSIUM DIHYDROGEN PHOSPHATE, PH 5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.69450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.69450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 27.12000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.34550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.12000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.34550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.69450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.12000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.34550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 36.69450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.12000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.34550 REMARK 290 SMTRY3 8 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: MONOMERIC 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 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 A 220 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 218 LIES ON A SPECIAL POSITION. 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 128 REMARK 465 ARG A 129 REMARK 465 ALA A 130 REMARK 465 ALA A 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 PRO A 60 -174.67 -69.24 REMARK 500 ARG A 87 -32.35 -130.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WN9 RELATED DB: PDB REMARK 900 ALTERNATIVE CRYSTAL FORM FOR THE SAME PROTEIN REMARK 900 RELATED ID: TTK003001805.2 RELATED DB: TARGETDB DBREF 1WNA A 1 131 UNP Q5SI52 Q5SI52_THET8 1 131 SEQRES 1 A 131 MSE VAL ARG VAL GLY MSE ARG ALA ALA PRO ARG VAL SER SEQRES 2 A 131 LEU GLU ALA LEU LYS ALA ALA LEU GLY GLY LEU LYS LEU SEQRES 3 A 131 SER GLU ALA LYS VAL TYR LEU ILE THR ASP TRP GLN ASP SEQRES 4 A 131 LYS ARG ASP GLN ALA ARG TYR ALA LEU LEU LEU HIS THR SEQRES 5 A 131 GLY LYS LYS ASP LEU LEU VAL PRO ASP ALA PHE GLY PRO SEQRES 6 A 131 ALA PHE PRO GLY GLY GLU GLU ALA LEU SER GLU LEU VAL SEQRES 7 A 131 GLY LEU LEU LEU ALA GLN GLY ALA ARG ARG PHE TYR GLU SEQRES 8 A 131 ALA VAL VAL SER PRO GLY GLU MSE THR ALA LEU LEU ASP SEQRES 9 A 131 LEU PRO PRO GLU GLU LEU LEU LYS ARG VAL MSE ALA ILE SEQRES 10 A 131 ALA ASN PRO THR ASP PRO GLY ILE TYR LEU LYS ARG ALA SEQRES 11 A 131 ALA MODRES 1WNA MSE A 1 MET SELENOMETHIONINE MODRES 1WNA MSE A 6 MET SELENOMETHIONINE MODRES 1WNA MSE A 99 MET SELENOMETHIONINE MODRES 1WNA MSE A 115 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 6 8 HET MSE A 99 8 HET MSE A 115 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 HOH *117(H2 O) HELIX 1 1 ALA A 9 GLY A 22 1 14 HELIX 2 2 GLY A 69 GLN A 84 1 16 HELIX 3 3 SER A 95 GLY A 97 5 3 HELIX 4 4 GLU A 98 ASP A 104 1 7 HELIX 5 5 PRO A 106 ALA A 118 1 13 HELIX 6 6 ASP A 122 LEU A 127 5 6 SHEET 1 A 6 VAL A 2 ARG A 3 0 SHEET 2 A 6 ASP A 56 PHE A 63 1 O LEU A 58 N VAL A 2 SHEET 3 A 6 TYR A 46 HIS A 51 -1 N LEU A 50 O LEU A 57 SHEET 4 A 6 LYS A 30 ASP A 36 -1 N LYS A 30 O HIS A 51 SHEET 5 A 6 ARG A 88 VAL A 94 1 O TYR A 90 N LEU A 33 SHEET 6 A 6 ASN A 119 PRO A 120 -1 O ASN A 119 N GLU A 91 LINK C MSE A 1 N VAL A 2 1555 1555 1.33 LINK C GLY A 5 N MSE A 6 1555 1555 1.33 LINK C MSE A 6 N ARG A 7 1555 1555 1.33 LINK C GLU A 98 N MSE A 99 1555 1555 1.33 LINK C MSE A 99 N THR A 100 1555 1555 1.33 LINK C VAL A 114 N MSE A 115 1555 1555 1.33 LINK C MSE A 115 N ALA A 116 1555 1555 1.33 CRYST1 54.240 70.691 73.389 90.00 90.00 90.00 C 2 2 21 8 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 0.018437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014146 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013626 0.00000 HETATM 1 N MSE A 1 17.432 22.692 28.578 1.00 48.94 N HETATM 2 CA MSE A 1 18.013 21.719 29.547 1.00 45.75 C HETATM 3 C MSE A 1 17.216 21.675 30.846 1.00 42.74 C HETATM 4 O MSE A 1 17.003 22.702 31.493 1.00 45.59 O HETATM 5 CB MSE A 1 19.461 22.088 29.862 1.00 48.12 C HETATM 6 CG MSE A 1 20.098 21.215 30.931 1.00 45.68 C HETATM 7 SE MSE A 1 21.861 21.824 31.410 1.00 44.87 SE HETATM 8 CE MSE A 1 21.371 23.171 32.704 1.00 43.81 C