HEADER TRANSFERASE 07-APR-03 1OYS
TITLE CRYSTAL STRUCTURE OF THE PHOSPHOROLYTIC EXORIBONUCLEASE RNASE PH FROM
TITLE 2 BACILLUS SUBTILIS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RIBONUCLEASE PH;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: RNASE PH, TRNA NUCLEOTIDYLTRANSFERASE;
COMPND 5 EC: 2.7.7.56;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS;
SOURCE 3 ORGANISM_TAXID: 1423;
SOURCE 4 GENE: RPH;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS TRANSFERASE, TRNA PROCESSING
EXPDTA X-RAY DIFFRACTION
AUTHOR L.S.HARLOW,A.KADZIOLA,K.F.JENSEN,S.LARSEN
REVDAT 4 14-FEB-24 1OYS 1 REMARK
REVDAT 3 27-OCT-21 1OYS 1 SEQADV
REVDAT 2 24-FEB-09 1OYS 1 VERSN
REVDAT 1 09-MAR-04 1OYS 0
JRNL AUTH L.S.HARLOW,A.KADZIOLA,K.F.JENSEN,S.LARSEN
JRNL TITL CRYSTAL STRUCTURE OF THE PHOSPHOROLYTIC EXORIBONUCLEASE
JRNL TITL 2 RNASE PH FROM BACILLUS SUBTILIS AND IMPLICATIONS FOR ITS
JRNL TITL 3 QUATERNARY STRUCTURE AND TRNA BINDING.
JRNL REF PROTEIN SCI. V. 13 668 2004
JRNL REFN ISSN 0961-8368
JRNL PMID 14767080
JRNL DOI 10.1110/PS.03477004
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
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) : 20.00
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) (%) : 98.5
REMARK 3 NUMBER OF REFLECTIONS : 16722
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.258
REMARK 3 FREE R VALUE : 0.284
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 848
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 : 1620
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
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) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
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) : 1.350 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.218 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.455 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.736 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1OYS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-03.
REMARK 100 THE DEPOSITION ID IS D_1000018812.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16768
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
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) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
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: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 72.29
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.47
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.50000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.61500
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.61500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.75000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.61500
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.61500
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 152.25000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.61500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.61500
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.75000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.61500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.61500
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 152.25000
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 101.50000
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: DIMERIC
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 350 BIOMT1 2 0.000000 -1.000000 0.000000 63.23000
REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 63.23000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 101.50000
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 PHE A 20
REMARK 465 ILE A 21
REMARK 465 SER A 22
REMARK 465 HIS A 23
REMARK 465 PRO A 24
REMARK 465 LEU A 66
REMARK 465 PRO A 67
REMARK 465 GLN A 68
REMARK 465 ALA A 69
REMARK 465 THR A 70
REMARK 465 ASN A 71
REMARK 465 GLN A 72
REMARK 465 GLN A 73
REMARK 465 THR A 74
REMARK 465 ILE A 75
REMARK 465 GLN A 76
REMARK 465 GLU A 77
REMARK 465 SER A 78
REMARK 465 SER A 79
REMARK 465 LYS A 80
REMARK 465 GLY A 81
REMARK 465 LYS A 82
REMARK 465 ILE A 83
REMARK 465 SER A 84
REMARK 465 GLY A 238
REMARK 465 ASP A 239
REMARK 465 SER A 240
REMARK 465 LEU A 241
REMARK 465 PRO A 242
REMARK 465 GLU A 243
REMARK 465 LEU A 244
REMARK 465 LYS A 245
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 ASP A 45 45.84 -82.24
REMARK 500 PHE A 50 4.18 -65.11
REMARK 500 ASP A 122 46.87 -143.99
REMARK 500 ASP A 175 81.39 58.32
REMARK 500 GLU A 206 -101.03 -57.83
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1OYP RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE PHOSPHOROLYTIC EXORIBONUCLEASE RNASE PH
REMARK 900 FROM BACILLUS SUBTILIS
REMARK 900 RELATED ID: 1OYR RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE PHOSPHOROLYTIC EXORIBONUCLEASE RNASE PH
REMARK 900 FROM BACILLUS SUBTILIS
DBREF 1OYS A 1 245 UNP P28619 RNPH_BACSU 1 245
SEQADV 1OYS GLN A 68 UNP P28619 ARG 68 ENGINEERED MUTATION
SEQADV 1OYS GLN A 73 UNP P28619 ARG 73 ENGINEERED MUTATION
SEQADV 1OYS GLN A 76 UNP P28619 ARG 76 ENGINEERED MUTATION
SEQRES 1 A 245 MET ARG HIS ASP GLY ARG GLN HIS ASP GLU LEU ARG PRO
SEQRES 2 A 245 ILE THR PHE ASP LEU ASP PHE ILE SER HIS PRO GLU GLY
SEQRES 3 A 245 SER VAL LEU ILE THR ALA GLY ASN THR LYS VAL ILE CYS
SEQRES 4 A 245 ASN ALA SER VAL GLU ASP ARG VAL PRO PRO PHE LEU ARG
SEQRES 5 A 245 GLY GLY GLY LYS GLY TRP ILE THR ALA GLU TYR SER MET
SEQRES 6 A 245 LEU PRO GLN ALA THR ASN GLN GLN THR ILE GLN GLU SER
SEQRES 7 A 245 SER LYS GLY LYS ILE SER GLY ARG THR MET GLU ILE GLN
SEQRES 8 A 245 ARG LEU ILE GLY ARG ALA LEU ARG ALA VAL VAL ASP LEU
SEQRES 9 A 245 GLU LYS LEU GLY GLU ARG THR ILE TRP ILE ASP CYS ASP
SEQRES 10 A 245 VAL ILE GLN ALA ASP GLY GLY THR ARG THR ALA SER ILE
SEQRES 11 A 245 THR GLY ALA PHE LEU ALA MET ALA ILE ALA ILE GLY LYS
SEQRES 12 A 245 LEU ILE LYS ALA GLY THR ILE LYS THR ASN PRO ILE THR
SEQRES 13 A 245 ASP PHE LEU ALA ALA ILE SER VAL GLY ILE ASP LYS GLU
SEQRES 14 A 245 GLN GLY ILE LEU LEU ASP LEU ASN TYR GLU GLU ASP SER
SEQRES 15 A 245 SER ALA GLU VAL ASP MET ASN VAL ILE MET THR GLY SER
SEQRES 16 A 245 GLY ARG PHE VAL GLU LEU GLN GLY THR GLY GLU GLU ALA
SEQRES 17 A 245 THR PHE SER ARG GLU ASP LEU ASN GLY LEU LEU GLY LEU
SEQRES 18 A 245 ALA GLU LYS GLY ILE GLN GLU LEU ILE ASP LYS GLN LYS
SEQRES 19 A 245 GLU VAL LEU GLY ASP SER LEU PRO GLU LEU LYS
HELIX 1 1 PRO A 48 ARG A 52 5 5
HELIX 2 2 GLY A 85 VAL A 101 1 17
HELIX 3 3 ASP A 103 GLY A 108 1 6
HELIX 4 4 GLY A 124 ALA A 147 1 24
HELIX 5 5 ASN A 177 ALA A 184 1 8
HELIX 6 6 SER A 211 LEU A 237 1 27
SHEET 1 A 5 ILE A 14 ASP A 17 0
SHEET 2 A 5 VAL A 28 ALA A 32 -1 O LEU A 29 N ASP A 17
SHEET 3 A 5 THR A 35 GLU A 44 -1 O CYS A 39 N VAL A 28
SHEET 4 A 5 THR A 111 GLN A 120 -1 O TRP A 113 N SER A 42
SHEET 5 A 5 TRP A 58 SER A 64 1 N GLU A 62 O ILE A 114
SHEET 1 B 4 GLY A 171 LEU A 174 0
SHEET 2 B 4 LEU A 159 ASP A 167 -1 N ASP A 167 O GLY A 171
SHEET 3 B 4 VAL A 186 THR A 193 -1 O MET A 188 N VAL A 164
SHEET 4 B 4 PHE A 198 GLY A 205 -1 O THR A 204 N ASP A 187
CRYST1 63.230 63.230 203.000 90.00 90.00 90.00 P 41 21 2 8
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 0.015815 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015815 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004926 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
