HEADER RNA BINDING PROTEIN 12-DEC-03 1V76 TITLE CRYSTAL STRUCTURE OF ARCHAEAL RIBONUCLEASE P PROTEIN PH1771P FROM TITLE 2 PYROCOCCUS HORIKOSHII OT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P PROTEIN PH1771P; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CORE REGION; COMPND 5 EC: 3.1.26.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 GENE: PH1771; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-22B KEYWDS RNA BINDING PROTEIN, ARCHAEAL RNASE P PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.NUMATA,Y.KAKUTA,M.KIMURA REVDAT 4 27-DEC-23 1V76 1 REMARK REVDAT 3 10-NOV-21 1V76 1 REMARK SEQADV REVDAT 2 24-FEB-09 1V76 1 VERSN REVDAT 1 05-OCT-04 1V76 0 JRNL AUTH T.NUMATA,I.ISHIMATSU,Y.KAKUTA,I.TANAKA,M.KIMURA JRNL TITL CRYSTAL STRUCTURE OF ARCHAEAL RIBONUCLEASE P PROTEIN PH1771P JRNL TITL 2 FROM PYROCOCCUS HORIKOSHII OT3: AN ARCHAEAL HOMOLOG OF JRNL TITL 3 EUKARYOTIC RIBONUCLEASE P PROTEIN RPP29 JRNL REF RNA V. 10 1423 2004 JRNL REFN ISSN 1355-8382 JRNL PMID 15317976 JRNL DOI 10.1261/RNA.7560904 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 205516.900 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 24588 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) : 0.209 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 2296 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3537 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 351 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1516 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.08000 REMARK 3 B22 (A**2) : -2.59000 REMARK 3 B33 (A**2) : 7.67000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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 : 0.37 REMARK 3 BSOL : 46.19 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 : SO4_XPLOR.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : SO4_XPLOR.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1V76 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000006291. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-03 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 : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97972, 0.90 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC (QUANTUM) REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25204 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M AMMONIUM SULFATE, 100MM TRIS-HCL, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.13550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 GLY A 32 REMARK 465 ALA A 33 REMARK 465 HIS A 34 REMARK 465 ARG A 35 REMARK 465 GLY B 32 REMARK 465 ALA B 33 REMARK 465 HIS B 34 REMARK 465 ARG B 35 REMARK 465 GLY B 36 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 ALA B 62 -134.33 -135.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PC0 RELATED DB: PDB REMARK 900 ARCHAEAL HOMOLOGUE OF RNASE P PROTEIN RPP29 DBREF 1V76 A 32 127 UNP O59425 RNP1_PYRHO 32 127 DBREF 1V76 B 32 127 UNP O59425 RNP1_PYRHO 32 127 SEQADV 1V76 SER A 93 UNP O59425 CYS 93 ENGINEERED MUTATION SEQADV 1V76 SER B 93 UNP O59425 CYS 93 ENGINEERED MUTATION SEQRES 1 A 96 GLY ALA HIS ARG GLY ARG VAL THR ARG ARG ASN ILE ILE SEQRES 2 A 96 TRP HIS GLU LEU ILE GLY LEU ARG VAL ARG ILE VAL GLY SEQRES 3 A 96 SER THR HIS PRO ALA PHE VAL GLY ILE GLU GLY TYR VAL SEQRES 4 A 96 ILE ASP GLU THR ARG ASN MET LEU VAL ILE ALA GLY ASP SEQRES 5 A 96 ARG ILE TRP LYS VAL PRO LYS ASP VAL SER ILE PHE GLU SEQRES 6 A 96 PHE GLU ALA ASP ASP GLY THR LYS ILE LYS ILE PRO GLY SEQRES 7 A 96 GLU ARG LEU VAL GLY ARG PRO GLU MET ARG LEU LYS LYS SEQRES 8 A 96 ARG TRP LYS LYS TRP SEQRES 1 B 96 GLY ALA HIS ARG GLY ARG VAL THR ARG ARG ASN ILE ILE SEQRES 2 B 96 TRP HIS GLU LEU ILE GLY LEU ARG VAL ARG ILE VAL GLY SEQRES 3 B 96 SER THR HIS PRO ALA PHE VAL GLY ILE GLU GLY TYR VAL SEQRES 4 B 96 ILE ASP GLU THR ARG ASN MET LEU VAL ILE ALA GLY ASP SEQRES 5 B 96 ARG ILE TRP LYS VAL PRO LYS ASP VAL SER ILE PHE GLU SEQRES 6 B 96 PHE GLU ALA ASP ASP GLY THR LYS ILE LYS ILE PRO GLY SEQRES 7 B 96 GLU ARG LEU VAL GLY ARG PRO GLU MET ARG LEU LYS LYS SEQRES 8 B 96 ARG TRP LYS LYS TRP HET SO4 A 502 5 HET SO4 B 501 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *144(H2 O) HELIX 1 1 ARG A 41 TRP A 45 5 5 HELIX 2 2 HIS A 60 VAL A 64 5 5 HELIX 3 3 GLU A 110 VAL A 113 5 4 HELIX 4 4 ARG A 115 LEU A 120 1 6 HELIX 5 5 LYS A 121 TRP A 124 5 4 HELIX 6 6 GLU B 110 VAL B 113 5 4 HELIX 7 7 ARG B 115 LEU B 120 1 6 HELIX 8 8 LYS B 121 TRP B 124 5 4 SHEET 1 A 6 ILE A 85 PRO A 89 0 SHEET 2 A 6 MET A 77 ALA A 81 -1 N ILE A 80 O TRP A 86 SHEET 3 A 6 GLU A 67 GLU A 73 -1 N TYR A 69 O ALA A 81 SHEET 4 A 6 ARG A 52 SER A 58 -1 N VAL A 53 O GLY A 68 SHEET 5 A 6 SER A 93 GLU A 98 -1 O ILE A 94 N GLY A 57 SHEET 6 A 6 LYS A 104 PRO A 108 -1 O ILE A 105 N PHE A 97 SHEET 1 B 6 ILE B 85 PRO B 89 0 SHEET 2 B 6 MET B 77 ALA B 81 -1 N ILE B 80 O TRP B 86 SHEET 3 B 6 GLU B 67 GLU B 73 -1 N TYR B 69 O ALA B 81 SHEET 4 B 6 ARG B 52 SER B 58 -1 N VAL B 53 O GLY B 68 SHEET 5 B 6 SER B 93 GLU B 98 -1 O ILE B 94 N GLY B 57 SHEET 6 B 6 LYS B 104 PRO B 108 -1 O ILE B 105 N PHE B 97 SITE 1 AC1 5 THR B 74 ARG B 75 ASN B 76 MET B 77 SITE 2 AC1 5 HOH B 566 SITE 1 AC2 4 THR A 74 ARG A 75 ASN A 76 MET A 77 CRYST1 24.133 56.271 71.756 90.00 96.80 90.00 P 1 21 1 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 0.041437 0.000000 0.004941 0.00000 SCALE2 0.000000 0.017771 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014035 0.00000