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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END