HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 29-MAY-04 1WJ9 TITLE CRYSTAL STRUCTURE OF A CRISPR-ASSOCIATED PROTEIN FROM THERMUS TITLE 2 THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRISPR-ASSOCIATED PROTEIN; 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 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 ALPHA AND BETA PROTEIN, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.EBIHARA,M.YAO,S.YOKOYAMA,S.KURAMITSU,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 13-MAR-24 1WJ9 1 REMARK REVDAT 3 24-FEB-09 1WJ9 1 VERSN REVDAT 2 26-SEP-06 1WJ9 1 JRNL REVDAT 1 29-NOV-04 1WJ9 0 JRNL AUTH A.EBIHARA,M.YAO,R.MASUI,I.TANAKA,S.YOKOYAMA,S.KURAMITSU JRNL TITL CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN TTHB192 FROM JRNL TITL 2 THERMUS THERMOPHILUS HB8 REVEALS A NEW PROTEIN FAMILY WITH JRNL TITL 3 AN RNA RECOGNITION MOTIF-LIKE DOMAIN JRNL REF PROTEIN SCI. V. 15 1494 2006 JRNL REFN ISSN 0961-8368 JRNL PMID 16672237 JRNL DOI 10.1110/PS.062131106 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1518252.710 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 22628 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) : 0.228 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2248 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 : 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) (%) : 98.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3401 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 362 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1505 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.70000 REMARK 3 B22 (A**2) : 5.30000 REMARK 3 B33 (A**2) : -10.00000 REMARK 3 B12 (A**2) : 4.30000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 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) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.110 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) : 1.440 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.260 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.350 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.680 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 26.16 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.PARAM REMARK 3 PARAMETER FILE 2 : WATER.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 1WJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023639. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-03; 05-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL26B2; BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000; 1.0800, 1.1052, 1.1056 REMARK 200 MONOCHROMATOR : SI DOUBLE-CRYSTAL; SI DOUBLE REMARK 200 -CRYSTAL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210; RIGAKU RAXIS REMARK 200 V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.6000 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; 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 (%): 60.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEGMME2000, 0.1M BICINE, PH 8.2, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.32933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.16467 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 43.74700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.58233 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.91167 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 ALA A 108 REMARK 465 ALA A 109 REMARK 465 THR A 110 REMARK 465 GLY A 111 REMARK 465 LYS A 112 REMARK 465 ARG A 113 REMARK 465 VAL A 114 REMARK 465 ALA A 115 REMARK 465 LEU A 116 REMARK 465 VAL A 156 REMARK 465 ARG A 157 REMARK 465 ARG A 158 REMARK 465 LYS A 159 REMARK 465 LYS A 160 REMARK 465 ASP A 161 REMARK 465 GLY A 162 REMARK 465 GLU A 163 REMARK 465 GLU A 164 REMARK 465 ALA A 165 REMARK 465 GLY A 166 REMARK 465 LYS A 167 REMARK 465 LEU A 168 REMARK 465 LEU A 169 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 A 33 36.66 -142.75 REMARK 500 PRO A 103 67.72 -61.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003001711.1 RELATED DB: TARGETDB DBREF 1WJ9 A 1 211 UNP Q53WG9 Q53WG9_THET8 1 211 SEQRES 1 A 211 MET TRP LEU THR LYS LEU VAL LEU ASN PRO ALA SER ARG SEQRES 2 A 211 ALA ALA ARG ARG ASP LEU ALA ASN PRO TYR GLU MET HIS SEQRES 3 A 211 ARG THR LEU SER LYS ALA VAL SER ARG ALA LEU GLU GLU SEQRES 4 A 211 GLY ARG GLU ARG LEU LEU TRP ARG LEU GLU PRO ALA ARG SEQRES 5 A 211 GLY LEU GLU PRO PRO VAL VAL LEU VAL GLN THR LEU THR SEQRES 6 A 211 GLU PRO ASP TRP SER VAL LEU ASP GLU GLY TYR ALA GLN SEQRES 7 A 211 VAL PHE PRO PRO LYS PRO PHE HIS PRO ALA LEU LYS PRO SEQRES 8 A 211 GLY GLN ARG LEU ARG PHE ARG LEU ARG ALA ASN PRO ALA SEQRES 9 A 211 LYS ARG LEU ALA ALA THR GLY LYS ARG VAL ALA LEU LYS SEQRES 10 A 211 THR PRO ALA GLU LYS VAL ALA TRP LEU GLU ARG ARG LEU SEQRES 11 A 211 GLU GLU GLY GLY PHE ARG LEU LEU GLU GLY GLU ARG GLY SEQRES 12 A 211 PRO TRP VAL GLN ILE LEU GLN ASP THR PHE LEU GLU VAL SEQRES 13 A 211 ARG ARG LYS LYS ASP GLY GLU GLU ALA GLY LYS LEU LEU SEQRES 14 A 211 GLN VAL GLN ALA VAL LEU PHE GLU GLY ARG LEU GLU VAL SEQRES 15 A 211 VAL ASP PRO GLU ARG ALA LEU ALA THR LEU ARG ARG GLY SEQRES 16 A 211 VAL GLY PRO GLY LYS ALA LEU GLY LEU GLY LEU LEU SER SEQRES 17 A 211 VAL ALA PRO FORMUL 2 HOH *100(H2 O) HELIX 1 1 SER A 12 ASN A 21 1 10 HELIX 2 2 ASN A 21 LYS A 31 1 11 HELIX 3 3 VAL A 33 GLU A 39 1 7 HELIX 4 4 ASP A 68 LEU A 72 5 5 HELIX 5 5 LYS A 117 GLY A 133 1 17 HELIX 6 6 ASP A 184 GLY A 195 1 12 SHEET 1 A 4 LEU A 45 LEU A 48 0 SHEET 2 A 4 VAL A 58 THR A 63 -1 O GLN A 62 N LEU A 45 SHEET 3 A 4 TRP A 2 LEU A 8 -1 N THR A 4 O VAL A 61 SHEET 4 A 4 ALA A 77 VAL A 79 -1 O GLN A 78 N VAL A 7 SHEET 1 B 4 LEU A 45 LEU A 48 0 SHEET 2 B 4 VAL A 58 THR A 63 -1 O GLN A 62 N LEU A 45 SHEET 3 B 4 TRP A 2 LEU A 8 -1 N THR A 4 O VAL A 61 SHEET 4 B 4 LYS A 83 PRO A 84 -1 O LYS A 83 N LEU A 3 SHEET 1 C 3 PHE A 135 LEU A 137 0 SHEET 2 C 3 VAL A 171 VAL A 182 -1 O GLU A 181 N ARG A 136 SHEET 3 C 3 VAL A 146 LEU A 154 -1 N THR A 152 O ALA A 173 SHEET 1 D 4 PHE A 135 LEU A 137 0 SHEET 2 D 4 VAL A 171 VAL A 182 -1 O GLU A 181 N ARG A 136 SHEET 3 D 4 ARG A 94 ALA A 101 -1 N LEU A 99 O PHE A 176 SHEET 4 D 4 SER A 208 ALA A 210 -1 O ALA A 210 N ARG A 96 SHEET 1 E 2 GLU A 139 GLY A 140 0 SHEET 2 E 2 GLY A 143 PRO A 144 -1 O GLY A 143 N GLY A 140 CRYST1 76.673 76.673 87.494 90.00 90.00 120.00 P 65 6 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 0.013042 0.007530 0.000000 0.00000 SCALE2 0.000000 0.015060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011429 0.00000