HEADER RNA BINDING PROTEIN 12-DEC-03 1V77 TITLE CRYSTAL STRUCTURE OF THE PH1877 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN PH1877; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PH1877P; COMPND 5 EC: 3.1.26.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 GENE: PH1877; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS RNASE P PROTEIN, TIM-BARREL, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.TAKAGI,T.NUMATA,Y.KAKUTA,M.KIMURA REVDAT 4 27-DEC-23 1V77 1 REMARK REVDAT 3 04-OCT-17 1V77 1 REMARK REVDAT 2 24-FEB-09 1V77 1 VERSN REVDAT 1 31-AUG-04 1V77 0 JRNL AUTH H.TAKAGI,M.WATANABE,Y.KAKUTA,R.KAMACHI,T.NUMATA,I.TANAKA, JRNL AUTH 2 M.KIMURA JRNL TITL CRYSTAL STRUCTURE OF THE RIBONUCLEASE P PROTEIN PH1877P FROM JRNL TITL 2 HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS HORIKOSHII OT3 JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 319 787 2004 JRNL REFN ISSN 0006-291X JRNL PMID 15184052 JRNL DOI 10.1016/J.BBRC.2004.05.055 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 893016.960 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 41080 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) : 0.230 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2052 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5970 REMARK 3 BIN R VALUE (WORKING SET) : 0.5540 REMARK 3 BIN FREE R VALUE : 0.5430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 317 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1669 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.76000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : -0.3 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.73 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 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) : 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.000 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.000 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 1.51 REMARK 3 BSOL : 13.51 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 1V77 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000006292. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-03 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 : 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) : 0.9792, 0.9795, 0.9870 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42142 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10700 REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20400 REMARK 200 FOR SHELL : 5.900 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 (%): 45.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22.5% PEG 6000, 0.1M HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 109.37600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.42650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.42650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 164.06400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.42650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.42650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.68800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.42650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.42650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 164.06400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.42650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.42650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.68800 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 109.37600 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 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 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 MET A 1 REMARK 465 VAL A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 209 REMARK 465 LEU A 210 REMARK 465 LYS A 211 REMARK 465 TYR A 212 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 13 88.81 -151.38 REMARK 500 GLU A 51 -77.31 -64.65 REMARK 500 SER A 102 62.60 36.15 REMARK 500 SER A 200 -81.82 -144.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 1V77 A 1 212 UNP O59543 RNP3_PYRHO 1 212 SEQRES 1 A 212 MET VAL GLY GLY GLY GLY VAL LYS PHE ILE GLU MET ASP SEQRES 2 A 212 ILE ARG ASP LYS GLU ALA TYR GLU LEU ALA LYS GLU TRP SEQRES 3 A 212 PHE ASP GLU VAL VAL VAL SER ILE LYS PHE ASN GLU GLU SEQRES 4 A 212 VAL ASP LYS GLU LYS LEU ARG GLU ALA ARG LYS GLU TYR SEQRES 5 A 212 GLY LYS VAL ALA ILE LEU LEU SER ASN PRO LYS PRO SER SEQRES 6 A 212 LEU VAL ARG ASP THR VAL GLN LYS PHE LYS SER TYR LEU SEQRES 7 A 212 ILE TYR VAL GLU SER ASN ASP LEU ARG VAL ILE ARG TYR SEQRES 8 A 212 SER ILE GLU LYS GLY VAL ASP ALA ILE ILE SER PRO TRP SEQRES 9 A 212 VAL ASN ARG LYS ASP PRO GLY ILE ASP HIS VAL LEU ALA SEQRES 10 A 212 LYS LEU MET VAL LYS LYS ASN VAL ALA LEU GLY PHE SER SEQRES 11 A 212 LEU ARG PRO LEU LEU TYR SER ASN PRO TYR GLU ARG ALA SEQRES 12 A 212 ASN LEU LEU ARG PHE MET MET LYS ALA TRP LYS LEU VAL SEQRES 13 A 212 GLU LYS TYR LYS VAL ARG ARG PHE LEU THR SER SER ALA SEQRES 14 A 212 GLN GLU LYS TRP ASP VAL ARG TYR PRO ARG ASP LEU ILE SEQRES 15 A 212 SER LEU GLY VAL VAL ILE GLY MET GLU ILE PRO GLN ALA SEQRES 16 A 212 LYS ALA SER ILE SER MET TYR PRO GLU ILE ILE LEU LYS SEQRES 17 A 212 ARG LEU LYS TYR FORMUL 2 HOH *225(H2 O) HELIX 1 1 ASP A 16 PHE A 27 1 12 HELIX 2 2 ASP A 41 GLY A 53 1 13 HELIX 3 3 LYS A 63 PHE A 74 1 12 HELIX 4 4 ASP A 85 LYS A 95 1 11 HELIX 5 5 ASP A 113 ASN A 124 1 12 HELIX 6 6 LEU A 131 SER A 137 1 7 HELIX 7 7 ASN A 138 LYS A 160 1 23 HELIX 8 8 GLU A 171 VAL A 175 5 5 HELIX 9 9 TYR A 177 ILE A 188 1 12 HELIX 10 10 GLU A 191 SER A 198 1 8 HELIX 11 11 SER A 200 LYS A 208 1 9 SHEET 1 A 7 ILE A 10 ILE A 14 0 SHEET 2 A 7 GLU A 29 PHE A 36 1 O VAL A 31 N GLU A 11 SHEET 3 A 7 VAL A 55 SER A 60 1 O ALA A 56 N ILE A 34 SHEET 4 A 7 LEU A 78 GLU A 82 1 O LEU A 78 N ILE A 57 SHEET 5 A 7 ALA A 99 ILE A 101 1 O ILE A 101 N VAL A 81 SHEET 6 A 7 ALA A 126 SER A 130 1 O GLY A 128 N ILE A 100 SHEET 7 A 7 ARG A 163 THR A 166 1 O PHE A 164 N PHE A 129 CRYST1 46.853 46.853 218.752 90.00 90.00 90.00 P 43 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 0.021343 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004571 0.00000