HEADER HYDROLASE 01-MAR-06 2DFE
TITLE CRYSTAL STRUCTURE OF TK-RNASE HII(1-200)-C
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RIBONUCLEASE HII;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: RNASE HII;
COMPND 5 EC: 3.1.26.4;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS;
SOURCE 3 ORGANISM_TAXID: 69014;
SOURCE 4 STRAIN: KOD1;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HB101;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJAL700K-C01
KEYWDS CHAMELEON SEQUENCE, RIBONUCLEASE HII, THERMOCOCCUS KODAKARAENSIS,
KEYWDS 2 FUSION PROTEIN, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.KATAGIRI,K.TAKANO,H.CHON,H.MATSUMURA,Y.KOGA,S.KANAYA
REVDAT 5 25-OCT-23 2DFE 1 REMARK
REVDAT 4 13-JUL-11 2DFE 1 VERSN
REVDAT 3 24-FEB-09 2DFE 1 VERSN
REVDAT 2 10-JUL-07 2DFE 1 JRNL
REVDAT 1 06-MAR-07 2DFE 0
JRNL AUTH K.TAKANO,Y.KATAGIRI,A.MUKAIYAMA,H.CHON,H.MATSUMURA,Y.KOGA,
JRNL AUTH 2 S.KANAYA
JRNL TITL CONFORMATIONAL CONTAGION IN A PROTEIN: STRUCTURAL PROPERTIES
JRNL TITL 2 OF A CHAMELEON SEQUENCE
JRNL REF PROTEINS V. 68 617 2007
JRNL REFN ISSN 0887-3585
JRNL PMID 17510955
JRNL DOI 10.1002/PROT.21451
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.0
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) : 2.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.28
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1313909.480
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 7709
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) : 0.227
REMARK 3 FREE R VALUE : 0.287
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 383
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015
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) : 2.40
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.40
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1232
REMARK 3 BIN R VALUE (WORKING SET) : 0.2730
REMARK 3 BIN FREE R VALUE : 0.3090
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 1.40
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 18
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.073
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1649
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 110
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 14.90
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.70
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.74000
REMARK 3 B22 (A**2) : -1.09000
REMARK 3 B33 (A**2) : -0.65000
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) : 0.29
REMARK 3 ESD FROM SIGMAA (A) : 0.24
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) : 0.40
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.100
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740
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) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.39
REMARK 3 BSOL : 40.75
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 2DFE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAR-06.
REMARK 100 THE DEPOSITION ID IS D_1000025353.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-NOV-05
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL41XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.00
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8628
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
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 (%) : 98.9
REMARK 200 DATA REDUNDANCY : NULL
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) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4
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: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 1IO2
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.07
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL SCREEN I SOLUTION NO. 6 (0.1M
REMARK 280 TRIS-HCL PH 8.5, 0.2M MGCL2, 30% PEG 4000), 100% GLYCEROL IN A 9:
REMARK 280 1 RATIO, VAPOR DIFFUSION, SITTING 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 30.78500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.29000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.99500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.29000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.78500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.99500
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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER GENERATED FROM THE
REMARK 300 MONOMER IN THE ASYMMETRIC UNIT.
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 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 LYS A 196 CG CD CE NZ
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 LEU A 80 32.08 -76.14
REMARK 500 LYS A 133 66.78 35.67
REMARK 500 GLU A 165 92.86 -65.16
REMARK 500 HIS A 187 -13.82 -156.22
REMARK 500 TRP A 198 -38.32 165.31
REMARK 500 GLN A 202 43.44 38.54
REMARK 500 MET A 204 47.59 -75.82
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1IO2 RELATED DB: PDB
REMARK 900 THE WILD FORM OF THE SAME PROTEIN
REMARK 900 RELATED ID: 2DFF RELATED DB: PDB
REMARK 900 THE LONGER VARIANT OF THE SAME PROTEIN
REMARK 900 RELATED ID: 2DFG RELATED DB: PDB
REMARK 900 THE LONGER VARIANT OF THE SAME PROTEIN
REMARK 900 RELATED ID: 2DFH RELATED DB: PDB
REMARK 900 THE LONGER VARIANT OF THE SAME PROTEIN
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE C-TERMINAL 9 RESIDUES, TQDMINKST ARE CHAMELEON
REMARK 999 SEQUENCEIN.
DBREF 2DFE A 1 200 UNP O74035 RNH2_PYRKO 1 200
SEQADV 2DFE THR A 201 UNP O74035 SEE REMARK 999
SEQADV 2DFE GLN A 202 UNP O74035 SEE REMARK 999
SEQADV 2DFE ASP A 203 UNP O74035 SEE REMARK 999
SEQADV 2DFE MET A 204 UNP O74035 SEE REMARK 999
SEQADV 2DFE ILE A 205 UNP O74035 SEE REMARK 999
SEQADV 2DFE ASN A 206 UNP O74035 SEE REMARK 999
SEQADV 2DFE LYS A 207 UNP O74035 SEE REMARK 999
SEQADV 2DFE SER A 208 UNP O74035 SEE REMARK 999
SEQADV 2DFE THR A 209 UNP O74035 SEE REMARK 999
SEQRES 1 A 209 MET LYS ILE ALA GLY ILE ASP GLU ALA GLY ARG GLY PRO
SEQRES 2 A 209 VAL ILE GLY PRO MET VAL ILE ALA ALA VAL VAL VAL ASP
SEQRES 3 A 209 GLU ASN SER LEU PRO LYS LEU GLU GLU LEU LYS VAL ARG
SEQRES 4 A 209 ASP SER LYS LYS LEU THR PRO LYS ARG ARG GLU LYS LEU
SEQRES 5 A 209 PHE ASN GLU ILE LEU GLY VAL LEU ASP ASP TYR VAL ILE
SEQRES 6 A 209 LEU GLU LEU PRO PRO ASP VAL ILE GLY SER ARG GLU GLY
SEQRES 7 A 209 THR LEU ASN GLU PHE GLU VAL GLU ASN PHE ALA LYS ALA
SEQRES 8 A 209 LEU ASN SER LEU LYS VAL LYS PRO ASP VAL ILE TYR ALA
SEQRES 9 A 209 ASP ALA ALA ASP VAL ASP GLU GLU ARG PHE ALA ARG GLU
SEQRES 10 A 209 LEU GLY GLU ARG LEU ASN PHE GLU ALA GLU VAL VAL ALA
SEQRES 11 A 209 LYS HIS LYS ALA ASP ASP ILE PHE PRO VAL VAL SER ALA
SEQRES 12 A 209 ALA SER ILE LEU ALA LYS VAL THR ARG ASP ARG ALA VAL
SEQRES 13 A 209 GLU LYS LEU LYS GLU GLU TYR GLY GLU ILE GLY SER GLY
SEQRES 14 A 209 TYR PRO SER ASP PRO ARG THR ARG ALA PHE LEU GLU ASN
SEQRES 15 A 209 TYR TYR ARG GLU HIS GLY GLU PHE PRO PRO ILE VAL ARG
SEQRES 16 A 209 LYS GLY TRP LYS THR THR GLN ASP MET ILE ASN LYS SER
SEQRES 17 A 209 THR
FORMUL 2 HOH *110(H2 O)
HELIX 1 1 SER A 29 LEU A 36 1 8
HELIX 2 2 LYS A 37 SER A 41 5 5
HELIX 3 3 THR A 45 GLY A 58 1 14
HELIX 4 4 PRO A 69 ILE A 73 5 5
HELIX 5 5 LEU A 80 SER A 94 1 15
HELIX 6 6 ASP A 110 ARG A 121 1 12
HELIX 7 7 PHE A 138 GLY A 164 1 27
HELIX 8 8 ASP A 173 GLU A 186 1 14
HELIX 9 9 ARG A 195 THR A 200 1 6
SHEET 1 A 5 ASP A 62 LEU A 68 0
SHEET 2 A 5 MET A 18 ASP A 26 -1 N MET A 18 O LEU A 68
SHEET 3 A 5 LYS A 2 ALA A 9 -1 N ILE A 3 O VAL A 25
SHEET 4 A 5 VAL A 101 ASP A 105 1 O TYR A 103 N ALA A 4
SHEET 5 A 5 GLU A 127 LYS A 131 1 O VAL A 129 N ALA A 104
CRYST1 61.570 67.990 44.580 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 0.016242 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014708 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022432 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
