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 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 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