HEADER TRANSFERASE 20-APR-07 2YWJ TITLE CRYSTAL STRUCTURE OF UNCHARACTERIZED CONSERVED PROTEIN FROM TITLE 2 METHANOCALDOCOCCUS JANNASCHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINE AMIDOTRANSFERASE SUBUNIT PDXT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UNCHARACTERIZED CONSERVED PROTEIN, GLUTAMINE COMPND 5 AMIDOTRANSFERASE GLUTAMINASE SUBUNIT PDXT; COMPND 6 EC: 2.6.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 243232; SOURCE 4 STRAIN: DSM 2661; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS UNCHARACTERIZED CONSERVED PROTEIN, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 2 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.MANZOKU,A.EBIHARA,S.YOKOYAMA,S.KURAMITSU,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 13-MAR-24 2YWJ 1 REMARK REVDAT 3 13-JUL-11 2YWJ 1 VERSN REVDAT 2 24-FEB-09 2YWJ 1 VERSN REVDAT 1 23-OCT-07 2YWJ 0 JRNL AUTH M.MANZOKU,A.EBIHARA,S.YOKOYAMA,S.KURAMITSU JRNL TITL CRYSTAL STRUCTURE OF UNCHARACTERIZED CONSERVED PROTEIN FROM JRNL TITL 2 METHANOCALDOCOCCUS JANNASCHII JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1093376.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13088 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) : 0.183 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1350 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1882 REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE : 0.2110 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 239 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1436 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.52000 REMARK 3 B22 (A**2) : -1.58000 REMARK 3 B33 (A**2) : -0.94000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.04 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.180 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) : 1.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.790 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.060 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.050 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 41.45 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 2YWJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027223. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI DOUBLE-CRYSTAL 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 : 13130 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.440 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG400, 100MM HEPES, 30% 1,2 REMARK 280 -PROPANEDIOL, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 22.40800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.20200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.23500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.20200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.40800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.23500 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: 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 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 186 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 ALA A 7 69.06 -158.05 REMARK 500 CYS A 75 -99.36 56.53 REMARK 500 LEU A 120 -68.60 -129.74 REMARK 500 ASP A 134 -86.90 -102.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MJA001001661.1 RELATED DB: TARGETDB DBREF 2YWJ A 1 186 UNP Q59055 PDXT_METJA 1 186 SEQRES 1 A 186 MET ILE ILE GLY VAL LEU ALA ILE GLN GLY ASP VAL GLU SEQRES 2 A 186 GLU HIS GLU GLU ALA ILE LYS LYS ALA GLY TYR GLU ALA SEQRES 3 A 186 LYS LYS VAL LYS ARG VAL GLU ASP LEU GLU GLY ILE ASP SEQRES 4 A 186 ALA LEU ILE ILE PRO GLY GLY GLU SER THR ALA ILE GLY SEQRES 5 A 186 LYS LEU MET LYS LYS TYR GLY LEU LEU GLU LYS ILE LYS SEQRES 6 A 186 ASN SER ASN LEU PRO ILE LEU GLY THR CYS ALA GLY MET SEQRES 7 A 186 VAL LEU LEU SER LYS GLY THR GLY ILE ASN GLN ILE LEU SEQRES 8 A 186 LEU GLU LEU MET ASP ILE THR VAL LYS ARG ASN ALA TYR SEQRES 9 A 186 GLY ARG GLN VAL ASP SER PHE GLU LYS GLU ILE GLU PHE SEQRES 10 A 186 LYS ASP LEU GLY LYS VAL TYR GLY VAL PHE ILE ARG ALA SEQRES 11 A 186 PRO VAL VAL ASP LYS ILE LEU SER ASP ASP VAL GLU VAL SEQRES 12 A 186 ILE ALA ARG ASP GLY ASP LYS ILE VAL GLY VAL LYS GLN SEQRES 13 A 186 GLY LYS TYR MET ALA LEU SER PHE HIS PRO GLU LEU SER SEQRES 14 A 186 GLU ASP GLY TYR LYS VAL TYR LYS TYR PHE VAL GLU ASN SEQRES 15 A 186 CYS VAL LYS LYS FORMUL 2 HOH *147(H2 O) HELIX 1 1 VAL A 12 ALA A 22 1 11 HELIX 2 2 ARG A 31 GLU A 36 5 6 HELIX 3 3 GLU A 47 TYR A 58 1 12 HELIX 4 4 GLY A 59 ASN A 66 1 8 HELIX 5 5 CYS A 75 SER A 82 1 8 HELIX 6 6 HIS A 165 SER A 169 5 5 HELIX 7 7 ASP A 171 VAL A 184 1 14 SHEET 1 A 7 GLU A 25 VAL A 29 0 SHEET 2 A 7 ILE A 2 LEU A 6 1 N ILE A 3 O GLU A 25 SHEET 3 A 7 ALA A 40 ILE A 43 1 O ILE A 42 N LEU A 6 SHEET 4 A 7 ILE A 71 THR A 74 1 O LEU A 72 N ILE A 43 SHEET 5 A 7 TYR A 159 LEU A 162 1 O MET A 160 N GLY A 73 SHEET 6 A 7 LYS A 150 GLN A 156 -1 N GLN A 156 O TYR A 159 SHEET 7 A 7 GLU A 142 ASP A 147 -1 N GLU A 142 O LYS A 155 SHEET 1 B 2 ILE A 97 LYS A 100 0 SHEET 2 B 2 VAL A 132 ILE A 136 -1 O VAL A 132 N LYS A 100 SHEET 1 C 2 PHE A 111 PHE A 117 0 SHEET 2 C 2 GLY A 121 PHE A 127 -1 O VAL A 123 N ILE A 115 CRYST1 44.816 50.470 70.404 90.00 90.00 90.00 P 21 21 21 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 0.022313 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014204 0.00000