HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 08-FEB-07 2EBE TITLE CRYSTAL STRUCTURE OF LYS11 TO MET MUTANT OF HYPOTHETICAL PROTEIN FROM TITLE 2 THERMUS THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN TTHA0061; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 GENE: TTHA0061; 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: PET-11A KEYWDS HYPOTHETICAL PROTEIN, TTHA0061, THERMUS THERMOPHILUS, STRUCTURAL KEYWDS 2 GENOMICS, UNKNOWN FUNCTION, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 3 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR T.S.KUMAREVEL,S.KURAMITSU,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 10-NOV-21 2EBE 1 SEQADV REVDAT 3 13-JUL-11 2EBE 1 VERSN REVDAT 2 24-FEB-09 2EBE 1 VERSN REVDAT 1 14-AUG-07 2EBE 0 JRNL AUTH T.S.KUMAREVEL,S.KURAMITSU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF LYS11 TO MET MUTANT OF HYPOTHETICAL JRNL TITL 2 PROTEIN FROM THERMUS THERMOPHILUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1165474.160 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21931 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) : 0.225 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1098 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3408 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 177 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1678 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -1.20000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.08 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.06 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 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) : 1.350 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.120 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.320 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.400 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 49.71 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : DNA-RNA_REP.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000026462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SI 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22011 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06500 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 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: 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 (%): 49.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 25% PEG 2000 MME, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 22.23000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.99500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.85500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.99500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.23000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.85500 REMARK 290 SMTRY3 4 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 GLN B 2 154.99 -46.77 REMARK 500 GLU B 71 27.20 -74.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EBG RELATED DB: PDB REMARK 900 RELATED ID: TTK003001907.2 RELATED DB: TARGETDB DBREF 2EBE A 1 106 UNP Q5SM82 Q5SM82_THET8 1 106 DBREF 2EBE B 1 106 UNP Q5SM82 Q5SM82_THET8 1 106 SEQADV 2EBE MET A 11 UNP Q5SM82 LEU 11 ENGINEERED MUTATION SEQADV 2EBE MET B 11 UNP Q5SM82 LEU 11 ENGINEERED MUTATION SEQRES 1 A 106 MET GLN ALA VAL ARG LEU PHE GLN GLY TYR MET TRP HIS SEQRES 2 A 106 PRO ARG ALA LEU ALA LEU ASP LEU LYS ALA LEU LEU PRO SEQRES 3 A 106 GLY GLU VAL ALA GLY ALA ARG LEU LEU TRP ASP GLU VAL SEQRES 4 A 106 PRO PRO PRO THR PRO PHE PHE GLU ASP GLY THR PRO THR SEQRES 5 A 106 HIS THR GLN ARG PHE TYR GLN LEU THR LEU LEU VAL LEU SEQRES 6 A 106 THR GLU GLU PRO PRO GLU ALA LEU LYS PRO LEU ALA GLU SEQRES 7 A 106 GLU ALA ALA GLU ALA LEU GLY GLU VAL LEU GLU GLY LEU SEQRES 8 A 106 PRO PRO GLU VAL GLY TRP LEU LEU LEU GLU ASP LEU ARG SEQRES 9 A 106 PRO LEU SEQRES 1 B 106 MET GLN ALA VAL ARG LEU PHE GLN GLY TYR MET TRP HIS SEQRES 2 B 106 PRO ARG ALA LEU ALA LEU ASP LEU LYS ALA LEU LEU PRO SEQRES 3 B 106 GLY GLU VAL ALA GLY ALA ARG LEU LEU TRP ASP GLU VAL SEQRES 4 B 106 PRO PRO PRO THR PRO PHE PHE GLU ASP GLY THR PRO THR SEQRES 5 B 106 HIS THR GLN ARG PHE TYR GLN LEU THR LEU LEU VAL LEU SEQRES 6 B 106 THR GLU GLU PRO PRO GLU ALA LEU LYS PRO LEU ALA GLU SEQRES 7 B 106 GLU ALA ALA GLU ALA LEU GLY GLU VAL LEU GLU GLY LEU SEQRES 8 B 106 PRO PRO GLU VAL GLY TRP LEU LEU LEU GLU ASP LEU ARG SEQRES 9 B 106 PRO LEU FORMUL 3 HOH *210(H2 O) HELIX 1 1 ASP A 20 LEU A 25 1 6 HELIX 2 2 PRO A 51 HIS A 53 5 3 HELIX 3 3 PRO A 69 ALA A 72 5 4 HELIX 4 4 LEU A 73 GLY A 90 1 18 HELIX 5 5 GLU A 101 LEU A 103 5 3 HELIX 6 6 ASP B 20 LEU B 25 1 6 HELIX 7 7 PRO B 69 ALA B 72 5 4 HELIX 8 8 LEU B 73 GLU B 89 1 17 HELIX 9 9 GLU B 101 LEU B 103 5 3 SHEET 1 A 5 GLU A 28 VAL A 29 0 SHEET 2 A 5 ALA A 32 VAL A 39 -1 O ALA A 32 N VAL A 29 SHEET 3 A 5 GLN A 55 THR A 66 -1 O THR A 61 N LEU A 35 SHEET 4 A 5 GLN A 2 PRO A 14 -1 N VAL A 4 O VAL A 64 SHEET 5 A 5 GLY A 96 LEU A 99 -1 O GLY A 96 N TRP A 12 SHEET 1 B 5 GLU B 28 VAL B 29 0 SHEET 2 B 5 ALA B 32 VAL B 39 -1 O ALA B 32 N VAL B 29 SHEET 3 B 5 GLN B 55 LEU B 65 -1 O GLN B 59 N ASP B 37 SHEET 4 B 5 ALA B 3 PRO B 14 -1 N GLN B 8 O LEU B 60 SHEET 5 B 5 GLY B 96 LEU B 99 -1 O GLY B 96 N TRP B 12 CRYST1 44.460 69.710 73.990 90.00 90.00 90.00 P 21 21 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 0.022492 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014345 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013515 0.00000