PDB Short entry for 1G8S HEADER RNA BINDING PROTEIN 20-NOV-00 1G8S TITLE METHANOCOCCUS JANNASCHII 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: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 GENE: 0697; 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: PET21A KEYWDS RRNA PROCESSING; RNA BINDING, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.C.BOISVERT,S.H.KIM REVDAT 4 09-AUG-23 1G8S 1 REMARK REVDAT 3 04-OCT-17 1G8S 1 REMARK REVDAT 2 24-FEB-09 1G8S 1 VERSN REVDAT 1 14-OCT-03 1G8S 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 HORIKSHII FIBRILLARIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.WANG,D.C.BOSIVERT,K.K.KIM,R.KIM,S.H.KIM REMARK 1 TITL CRYSTAL STRUCTURE OF A FIBRILLARIN HOMOLOGUE FROM REMARK 1 TITL 2 METHANOCOCCUS JANNASCHII, A HYPERTHERMOPHILE, AT 1.6 REMARK 1 TITL 3 ANGSTROMS RESOLUTION REMARK 1 REF EMBO J. V. 19 317 2000 REMARK 1 REFN ISSN 0261-4189 REMARK 1 DOI 10.1093/EMBOJ/19.3.317 REMARK 2 REMARK 2 RESOLUTION. 1.60 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.001 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 966006.530 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 68772 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) : 0.201 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3409 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9632 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 465 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1829 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.57000 REMARK 3 B22 (A**2) : 4.80000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.37000 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) : 0.22 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) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 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) : 1.890 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.950 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.410 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.280 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 55.73 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: PROBE PROGRAM WAS USED TO IDENTIFY REMARK 3 RESIDUES INCORRECTLY REFINED BY CNS REMARK 4 REMARK 4 1G8S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-00. REMARK 100 THE DEPOSITION ID IS D_1000012375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-97 REMARK 200 TEMPERATURE (KELVIN) : 170 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97894 REMARK 200 MONOCHROMATOR : MONOCHROMATIC REMARK 200 OPTICS : MONOCHROMATIC REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO SUITE REMARK 200 DATA SCALING SOFTWARE : SCALEPACK SUITE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68772 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.07600 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) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1FBN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 20% ISOPROPANOL, 0.1 M REMARK 280 NACITRATE, 25 MG/ML FIBRILLARIN, PH 5.6, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 273K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 60.57600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.60600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.57600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.60600 REMARK 290 SMTRY3 4 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: 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 -1.000000 0.000000 0.000000 114.44430 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 54.78791 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 PHE A 10 -126.22 49.79 REMARK 500 THR A 87 -70.83 -53.10 REMARK 500 GLU A 120 -15.76 88.73 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 MET A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FBN RELATED DB: PDB REMARK 900 1FBN IS THE SAME PROTEIN BUT WITHOUT A REFINED METHIONINE AS PART REMARK 900 OF THE STRUCTURE REMARK 900 RELATED ID: 1G8A RELATED DB: PDB REMARK 900 1G8A CONTAINS THE SAME PROTEIN BUT FROM A DIFFERENT SOURCE DBREF 1G8S A 1 230 UNP Q58108 FLPA_METJA 1 230 SEQRES 1 A 230 MET GLU ASP ILE LYS ILE LYS GLU ILE PHE GLU ASN ILE SEQRES 2 A 230 TYR GLU VAL ASP LEU GLY ASP GLY LEU LYS ARG ILE ALA SEQRES 3 A 230 THR LYS SER ILE VAL LYS GLY LYS LYS VAL TYR ASP GLU SEQRES 4 A 230 LYS ILE ILE LYS ILE GLY ASP GLU GLU TYR ARG ILE TRP SEQRES 5 A 230 ASN PRO ASN LYS SER LYS LEU ALA ALA ALA ILE ILE LYS SEQRES 6 A 230 GLY LEU LYS VAL MET PRO ILE LYS ARG ASP SER LYS ILE SEQRES 7 A 230 LEU TYR LEU GLY ALA SER ALA GLY THR THR PRO SER HIS SEQRES 8 A 230 VAL ALA ASP ILE ALA ASP LYS GLY ILE VAL TYR ALA ILE SEQRES 9 A 230 GLU TYR ALA PRO ARG ILE MET ARG GLU LEU LEU ASP ALA SEQRES 10 A 230 CYS ALA GLU ARG GLU ASN ILE ILE PRO ILE LEU GLY ASP SEQRES 11 A 230 ALA ASN LYS PRO GLN GLU TYR ALA ASN ILE VAL GLU LYS SEQRES 12 A 230 VAL ASP VAL ILE TYR GLU ASP VAL ALA GLN PRO ASN GLN SEQRES 13 A 230 ALA GLU ILE LEU ILE LYS ASN ALA LYS TRP PHE LEU LYS SEQRES 14 A 230 LYS GLY GLY TYR GLY MET ILE ALA ILE LYS ALA ARG SER SEQRES 15 A 230 ILE ASP VAL THR LYS ASP PRO LYS GLU ILE PHE LYS GLU SEQRES 16 A 230 GLN LYS GLU ILE LEU GLU ALA GLY GLY PHE LYS ILE VAL SEQRES 17 A 230 ASP GLU VAL ASP ILE GLU PRO PHE GLU LYS ASP HIS VAL SEQRES 18 A 230 MET PHE VAL GLY ILE TRP GLU GLY LYS HET MET A 500 9 HETNAM MET METHIONINE FORMUL 2 MET C5 H11 N O2 S FORMUL 3 HOH *140(H2 O) HELIX 1 1 SER A 57 LYS A 65 1 9 HELIX 2 2 GLY A 86 ALA A 96 1 11 HELIX 3 3 ALA A 107 CYS A 118 1 12 HELIX 4 4 LYS A 133 ALA A 138 5 6 HELIX 5 5 ASN A 155 PHE A 167 1 13 HELIX 6 6 ARG A 181 ILE A 183 5 3 HELIX 7 7 ASP A 188 GLY A 204 1 17 SHEET 1 A 5 LYS A 5 ILE A 9 0 SHEET 2 A 5 ILE A 13 ASP A 17 -1 O ILE A 13 N ILE A 9 SHEET 3 A 5 ARG A 24 LYS A 28 -1 O ARG A 24 N VAL A 16 SHEET 4 A 5 GLU A 47 ILE A 51 -1 N ARG A 50 O THR A 27 SHEET 5 A 5 ILE A 41 ILE A 44 -1 O ILE A 42 N TYR A 49 SHEET 1 B 7 ILE A 124 LEU A 128 0 SHEET 2 B 7 ILE A 100 GLU A 105 1 O VAL A 101 N ILE A 125 SHEET 3 B 7 LYS A 77 LEU A 81 1 O ILE A 78 N TYR A 102 SHEET 4 B 7 VAL A 144 GLU A 149 1 N ASP A 145 O LYS A 77 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 220 TRP A 227 -1 O VAL A 221 N ILE A 178 SHEET 7 B 7 PHE A 205 ASP A 212 -1 O LYS A 206 N ILE A 226 CISPEP 1 GLU A 214 PRO A 215 0 0.17 SITE 1 AC1 11 LYS A 56 LYS A 58 TYR A 80 SER A 84 SITE 2 AC1 11 ALA A 85 THR A 87 THR A 88 PRO A 89 SITE 3 AC1 11 ASP A 150 HOH A 517 HOH A 525 CRYST1 121.152 43.212 55.197 90.00 96.98 90.00 C 1 2 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 0.008254 0.000000 0.001011 0.00000 SCALE2 0.000000 0.023142 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018252 0.00000