HEADER RNA BINDING PROTEIN 16-NOV-00 1G8A TITLE PYROCOCCUS HORIKOSHII FIBRILLARIN PRE-RRNA PROCESSING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRILLARIN-LIKE PRE-RRNA PROCESSING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 GENE: 0048; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS RRNA BINDING, RNA BINDING, STRUCTURAL GENOMICS, BSGC STRUCTURE FUNDED KEYWDS 2 BY NIH, PROTEIN STRUCTURE INITIATIVE, PSI, BERKELEY STRUCTURAL KEYWDS 3 GENOMICS CENTER, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.C.BOISVERT,S.H.KIM,BERKELEY STRUCTURAL GENOMICS CENTER (BSGC) REVDAT 7 09-AUG-23 1G8A 1 REMARK REVDAT 6 31-JAN-18 1G8A 1 REMARK REVDAT 5 04-OCT-17 1G8A 1 REMARK REVDAT 4 24-FEB-09 1G8A 1 VERSN REVDAT 3 25-JAN-05 1G8A 1 AUTHOR KEYWDS REMARK REVDAT 2 24-AUG-04 1G8A 1 KEYWDS REVDAT 1 14-OCT-03 1G8A 0 JRNL AUTH D.C.BOISVERT,S.H.KIM JRNL TITL A STRUCTURAL APPROACH TO GENE FUNCTION AND STRUCTURE QUALITY JRNL TITL 2 FOR PYROCOCCUS HORIKOSHII FIBRILLARIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 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 : MLF REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 471722.300 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 37696 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) : 0.203 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1879 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4453 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 260 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1825 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 407 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.06 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) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.07 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) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 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) : 1.130 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.740 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.550 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.450 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 38.17 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 1G8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-00. REMARK 100 THE DEPOSITION ID IS D_1000012358. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : STANDARD AT ALS 5.0.2 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO SUITE REMARK 200 DATA SCALING SOFTWARE : SCALEPACK SUITE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.06000 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: EPMR REMARK 200 STARTING MODEL: 1FIB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NACL, 50 MM TRIS, 85 MG/ML REMARK 280 FIBRILLARIN, PH 7.5, COOLING, TEMPERATURE 4K, TEMPERATURE 277.0K 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 20.54900 REMARK 290 SMTRY3 2 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 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 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 17 -146.34 -102.11 REMARK 500 ASP A 184 109.81 -162.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G8S RELATED DB: PDB REMARK 900 1G8S CONTAINS THE SAME PROTEIN BUT FROM A DIFFERENT SOURCE REMARK 900 RELATED ID: BSGCAIR30655 RELATED DB: TARGETDB DBREF 1G8A A 1 227 UNP O57811 FLPA_PYRHO 1 227 SEQRES 1 A 227 MET VAL GLU VAL LYS LYS HIS LYS PHE PRO GLY VAL TYR SEQRES 2 A 227 THR VAL ILE ASP ASP ASP GLY SER GLU ARG ILE ALA THR SEQRES 3 A 227 LYS ASN LEU VAL PRO GLY GLN ARG VAL TYR GLY GLU ARG SEQRES 4 A 227 VAL ILE LYS TRP GLU GLY GLU GLU TYR ARG ILE TRP ASN SEQRES 5 A 227 PRO ASN ARG SER LYS LEU GLY ALA ALA ILE MET ASN GLY SEQRES 6 A 227 LEU LYS ASN PHE PRO ILE LYS PRO GLY LYS SER VAL LEU SEQRES 7 A 227 TYR LEU GLY ILE ALA SER GLY THR THR ALA SER HIS VAL SEQRES 8 A 227 SER ASP ILE VAL GLY TRP GLU GLY LYS ILE PHE GLY ILE SEQRES 9 A 227 GLU PHE SER PRO ARG VAL LEU ARG GLU LEU VAL PRO ILE SEQRES 10 A 227 VAL GLU GLU ARG ARG ASN ILE VAL PRO ILE LEU GLY ASP SEQRES 11 A 227 ALA THR LYS PRO GLU GLU TYR ARG ALA LEU VAL PRO LYS SEQRES 12 A 227 VAL ASP VAL ILE PHE GLU ASP VAL ALA GLN PRO THR GLN SEQRES 13 A 227 ALA LYS ILE LEU ILE ASP ASN ALA GLU VAL TYR LEU LYS SEQRES 14 A 227 ARG GLY GLY TYR GLY MET ILE ALA VAL LYS SER ARG SER SEQRES 15 A 227 ILE ASP VAL THR LYS GLU PRO GLU GLN VAL PHE ARG GLU SEQRES 16 A 227 VAL GLU ARG GLU LEU SER GLU TYR PHE GLU VAL ILE GLU SEQRES 17 A 227 ARG LEU ASN LEU GLU PRO TYR GLU LYS ASP HIS ALA LEU SEQRES 18 A 227 PHE VAL VAL ARG LYS THR FORMUL 2 HOH *407(H2 O) HELIX 1 1 SER A 56 ASN A 64 1 9 HELIX 2 2 THR A 86 GLY A 96 1 11 HELIX 3 3 SER A 107 GLU A 119 1 13 HELIX 4 4 LYS A 133 ARG A 138 5 6 HELIX 5 5 THR A 155 TYR A 167 1 13 HELIX 6 6 ARG A 181 ILE A 183 5 3 HELIX 7 7 GLU A 188 GLU A 202 1 15 SHEET 1 A 5 GLU A 3 LYS A 6 0 SHEET 2 A 5 VAL A 12 ILE A 16 -1 N THR A 14 O LYS A 5 SHEET 3 A 5 ARG A 23 LYS A 27 -1 O ARG A 23 N VAL A 15 SHEET 4 A 5 GLU A 46 ILE A 50 -1 N ARG A 49 O THR A 26 SHEET 5 A 5 VAL A 40 TRP A 43 -1 N ILE A 41 O TYR A 48 SHEET 1 B 7 ILE A 124 LEU A 128 0 SHEET 2 B 7 LYS A 100 GLU A 105 1 O ILE A 101 N VAL A 125 SHEET 3 B 7 SER A 76 LEU A 80 1 O VAL A 77 N PHE A 102 SHEET 4 B 7 VAL A 144 GLU A 149 1 N ASP A 145 O SER A 76 SHEET 5 B 7 LEU A 168 LYS A 179 1 N LYS A 169 O VAL A 144 SHEET 6 B 7 HIS A 219 ARG A 225 -1 O ALA A 220 N VAL A 178 SHEET 7 B 7 GLU A 205 ASN A 211 -1 N GLU A 205 O ARG A 225 CISPEP 1 GLU A 213 PRO A 214 0 0.34 CRYST1 46.376 41.098 54.168 90.00 98.26 90.00 P 1 21 1 2 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 0.021563 0.000000 0.003130 0.00000 SCALE2 0.000000 0.024332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018655 0.00000