HEADER HYDROLASE 01-NOV-11 3UFC TITLE CHARACTERIZATION OF A CAS6-RELATED GENE FROM PYROCOCCUS FURIOSUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: CAS6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 186497; SOURCE 4 STRAIN: ATCC 43587 / DSM 3638 / JCM 8422 / VC1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS CAS6, FERREDOXIN-LIKE DOMAIN, RNA BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.M.PARK,J.S.KIM REVDAT 3 20-MAR-24 3UFC 1 SEQADV REVDAT 2 03-JUL-13 3UFC 1 JRNL REVDAT 1 21-MAR-12 3UFC 0 JRNL AUTH H.M.PARK,M.SHIN,J.SUN,G.S.KIM,Y.C.LEE,J.H.PARK,B.Y.KIM, JRNL AUTH 2 J.S.KIM JRNL TITL CRYSTAL STRUCTURE OF A CAS6 PARALOGOUS PROTEIN FROM JRNL TITL 2 PYROCOCCUS FURIOSUS JRNL REF PROTEINS V. 80 1895 2012 JRNL REFN ISSN 0887-3585 JRNL PMID 22447673 JRNL DOI 10.1002/PROT.24061 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 26932 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2166 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1986 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.40900 REMARK 3 B22 (A**2) : 4.40900 REMARK 3 B33 (A**2) : -8.81900 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.257 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.623 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.629 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.348 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.724 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 102.9 REMARK 3 BSOL : NULL 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_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 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.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 3UFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068683. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-11 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 : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1159 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26932 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 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 (%) : 94.2 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL 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) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) POLYETHYLENE GLYCOL 400, REMARK 280 0.1M HEPES-NA, 0.1M MAGNESIUM CHLORIDE HEXAHYDRATE , PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 39.12067 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 78.24133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 78.24133 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 39.12067 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: X 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN X 241 CG CD OE1 NE2 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 GLU X 36 88.18 -153.29 REMARK 500 LYS X 66 -48.65 -150.47 REMARK 500 GLU X 140 78.21 -160.50 REMARK 500 LYS X 196 -85.25 70.65 REMARK 500 GLU X 240 106.84 -173.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I4H RELATED DB: PDB REMARK 900 CAS6 IS AN ENDORIBONUCLEASE THAT GENERATES GUIDE RNAS FOR INVADER REMARK 900 DEFENSE IN PROKARYOTES DBREF 3UFC X 1 241 UNP Q8U3R3 Q8U3R3_PYRFU 1 241 SEQADV 3UFC GLY X -1 UNP Q8U3R3 EXPRESSION TAG SEQADV 3UFC GLY X 0 UNP Q8U3R3 EXPRESSION TAG SEQRES 1 X 243 GLY GLY MET ARG ILE GLU ILE LYS LEU LEU PRO LEU GLN SEQRES 2 X 243 ASP ASN PRO VAL ILE PRO PHE ASN TYR ASN TYR GLU LEU SEQRES 3 X 243 TYR SER GLN ILE VAL GLU LYS ALA GLY ALA ILE GLU PRO SEQRES 4 X 243 ARG ILE VAL LYS LEU LEU GLU SER PRO HIS GLY TYR TRP SEQRES 5 X 243 THR PHE SER ARG ILE ILE ILE ARG LYS ARG GLU ILE ILE SEQRES 6 X 243 PRO GLU LYS GLY ILE LYS ILE LEU SER ASP ASP ILE SER SEQRES 7 X 243 LEU TYR ILE SER SER SER ASN LYS GLU ILE ILE LYS GLY SEQRES 8 X 243 ILE VAL GLU GLY ILE GLU LYS SER PRO GLU PHE LYS ILE SEQRES 9 X 243 GLY ASP VAL GLY PHE LEU VAL ALA ASP ILE LYS ALA LEU SEQRES 10 X 243 LYS SER LYS GLU ILE LYS ASN VAL ASN ILE PHE SER THR SEQRES 11 X 243 LEU SER PRO ILE VAL VAL ARG THR VAL LYS PHE GLU GLY SEQRES 12 X 243 ASP LYS LEU LYS HIS TRP ASP LEU TYR PRO HIS ASP GLU SEQRES 13 X 243 LEU PHE LEU ASP ARG LEU ARG LYS VAL MET LEU LEU ARG SEQRES 14 X 243 TYR HIS GLU VAL MET GLY ASP LEU PRO GLU ASP LYS ASP SEQRES 15 X 243 PHE ARG ILE GLU LEU ILE LYS PHE LYS PRO THR ARG LEU SEQRES 16 X 243 ILE VAL LYS ASP SER TYR ILE ARG GLY SER LEU MET VAL SEQRES 17 X 243 PHE ARG TYR TYR GLY SER LYS GLU ILE ALA LYS PHE GLY SEQRES 18 X 243 TYR GLU ASN GLY PHE GLY GLU LYS THR ASN LEU GLY PHE SEQRES 19 X 243 GLY MET VAL LYS ILE ILE GLU GLU GLN FORMUL 2 HOH *179(H2 O) HELIX 1 1 TYR X 20 GLU X 36 1 17 HELIX 2 2 ILE X 39 SER X 45 1 7 HELIX 3 3 ASN X 83 SER X 97 1 15 HELIX 4 4 LEU X 155 GLY X 173 1 19 HELIX 5 5 SER X 212 GLY X 223 1 12 HELIX 6 6 LYS X 227 GLY X 231 5 5 SHEET 1 A 3 THR X 51 PHE X 52 0 SHEET 2 A 3 ILE X 75 SER X 81 -1 O SER X 80 N THR X 51 SHEET 3 A 3 ILE X 56 ILE X 57 -1 N ILE X 56 O SER X 76 SHEET 1 B 5 THR X 51 PHE X 52 0 SHEET 2 B 5 ILE X 75 SER X 81 -1 O SER X 80 N THR X 51 SHEET 3 B 5 MET X 1 PRO X 9 -1 N ILE X 3 O ILE X 79 SHEET 4 B 5 VAL X 105 ALA X 114 -1 O LYS X 113 N GLU X 4 SHEET 5 B 5 GLU X 99 ILE X 102 -1 N ILE X 102 O VAL X 105 SHEET 1 C 3 VAL X 15 ILE X 16 0 SHEET 2 C 3 GLY X 67 ILE X 70 -1 O ILE X 68 N ILE X 16 SHEET 3 C 3 ARG X 60 ILE X 63 -1 N GLU X 61 O LYS X 69 SHEET 1 D 4 PHE X 181 VAL X 195 0 SHEET 2 D 4 SER X 198 GLY X 211 -1 O SER X 198 N VAL X 195 SHEET 3 D 4 VAL X 123 THR X 128 -1 N ASN X 124 O TYR X 209 SHEET 4 D 4 VAL X 235 ILE X 237 -1 O LYS X 236 N SER X 127 SHEET 1 E 2 VAL X 134 GLU X 140 0 SHEET 2 E 2 LYS X 143 LEU X 149 -1 O LEU X 149 N VAL X 134 CRYST1 79.805 79.805 117.362 90.00 90.00 120.00 P 31 2 1 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 0.012531 0.007235 0.000000 0.00000 SCALE2 0.000000 0.014469 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008521 0.00000