HEADER TRANSLATION 07-MAY-07 2Z0X TITLE CRYSTAL STRUCTURE OF PROX-CYSSA COMPLEX FROM T. THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN TTHA1699; COMPND 3 CHAIN: A; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS PROTEIN-CYSSA COMPLEX, TRANSLATION, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 2 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR K.MURAYAMA,M.KATO-MURAYAMA,T.TERADA,S.KURAMITSU,M.SHIROUZU, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 01-NOV-23 2Z0X 1 REMARK REVDAT 2 24-FEB-09 2Z0X 1 VERSN REVDAT 1 13-NOV-07 2Z0X 0 JRNL AUTH K.MURAYAMA,M.KATO-MURAYAMA,T.TERADA,M.SHIROUZU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF PROX-CYSSA COMPLEX FROM T. THERMOPHILUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.64 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1095505.740 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 16172 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) : 0.158 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 788 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) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2150 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 111 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1161 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.25000 REMARK 3 B22 (A**2) : 0.41000 REMARK 3 B33 (A**2) : -0.15000 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) : 0.14 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) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.390 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) : 1.790 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.410 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.370 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.620 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.29 REMARK 3 BSOL : 25.18 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 : CYSSA.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z0X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000027381. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16242 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 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 (%) : 96.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02200 REMARK 200 FOR THE DATA SET : 59.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.07900 REMARK 200 FOR SHELL : 11.60 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: PDB ENTRY 2CX5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 0.1M HEPES, 30MM CYSSA, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING 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 15.75600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.87900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.30650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.87900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.75600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.30650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 8 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5CA A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003001048.5 RELATED DB: TARGETDB DBREF 2Z0X A 1 158 UNP Q5SHN1 Q5SHN1_THET8 1 158 SEQRES 1 A 158 MET SER LEU SER PRO SER ALA ARG ARG VAL GLN GLY ALA SEQRES 2 A 158 LEU GLU THR ARG GLY PHE GLY HIS LEU LYS VAL VAL GLU SEQRES 3 A 158 LEU PRO ALA SER THR ARG THR ALA LYS GLU ALA ALA GLN SEQRES 4 A 158 ALA VAL GLY ALA GLU VAL GLY GLN ILE VAL LYS SER LEU SEQRES 5 A 158 VAL PHE VAL GLY GLU LYS GLY ALA TYR LEU PHE LEU VAL SEQRES 6 A 158 SER GLY LYS ASN ARG LEU ASP LEU GLY LYS ALA THR ARG SEQRES 7 A 158 LEU VAL GLY GLY PRO LEU ARG GLN ALA THR PRO GLU GLU SEQRES 8 A 158 VAL ARG GLU LEU THR GLY PHE ALA ILE GLY GLY VAL PRO SEQRES 9 A 158 PRO VAL GLY HIS ASN THR PRO LEU PRO ALA TYR LEU ASP SEQRES 10 A 158 GLU ASP LEU LEU GLY TYR PRO GLU VAL TRP ALA ALA GLY SEQRES 11 A 158 GLY THR PRO ARG ALA LEU PHE ARG ALA THR PRO LYS GLU SEQRES 12 A 158 LEU LEU ALA LEU THR GLY ALA GLN VAL ALA ASP LEU LYS SEQRES 13 A 158 GLU GLY HET 5CA A 200 29 HETNAM 5CA 5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE FORMUL 2 5CA C13 H19 N7 O7 S2 FORMUL 3 HOH *255(H2 O) HELIX 1 1 SER A 4 ARG A 17 1 14 HELIX 2 2 THR A 33 GLY A 42 1 10 HELIX 3 3 GLU A 44 GLY A 46 5 3 HELIX 4 4 ASP A 72 GLY A 81 1 10 HELIX 5 5 THR A 88 GLY A 97 1 10 HELIX 6 6 ASP A 119 TYR A 123 5 5 HELIX 7 7 THR A 140 GLY A 149 1 10 SHEET 1 A 5 VAL A 24 GLU A 26 0 SHEET 2 A 5 ALA A 135 ALA A 139 -1 O LEU A 136 N VAL A 25 SHEET 3 A 5 VAL A 126 ALA A 129 -1 N VAL A 126 O ALA A 139 SHEET 4 A 5 ILE A 48 GLY A 56 1 N VAL A 49 O TRP A 127 SHEET 5 A 5 LEU A 84 GLN A 86 -1 O ARG A 85 N VAL A 55 SHEET 1 B 7 VAL A 24 GLU A 26 0 SHEET 2 B 7 ALA A 135 ALA A 139 -1 O LEU A 136 N VAL A 25 SHEET 3 B 7 VAL A 126 ALA A 129 -1 N VAL A 126 O ALA A 139 SHEET 4 B 7 ILE A 48 GLY A 56 1 N VAL A 49 O TRP A 127 SHEET 5 B 7 ALA A 60 SER A 66 -1 O VAL A 65 N LYS A 50 SHEET 6 B 7 ALA A 114 ASP A 117 1 O TYR A 115 N LEU A 64 SHEET 7 B 7 GLN A 151 ALA A 153 1 O GLN A 151 N LEU A 116 SITE 1 AC1 26 THR A 31 ARG A 32 ILE A 48 VAL A 49 SITE 2 AC1 26 LYS A 50 SER A 51 LEU A 52 ARG A 78 SITE 3 AC1 26 GLN A 86 ALA A 87 PRO A 89 ILE A 100 SITE 4 AC1 26 GLY A 101 GLU A 157 GLY A 158 HOH A 201 SITE 5 AC1 26 HOH A 218 HOH A 243 HOH A 249 HOH A 257 SITE 6 AC1 26 HOH A 259 HOH A 261 HOH A 273 HOH A 309 SITE 7 AC1 26 HOH A 327 HOH A 341 CRYST1 31.512 50.613 81.758 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 0.031734 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019758 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012231 0.00000