HEADER TRANSFERASE 20-JUN-03 1PRY TITLE STRUCTURE DETERMINATION OF FIBRILLARIN HOMOLOGUE FROM TITLE 2 HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS FURIOSUS (PFU-65527) 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 FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 GENE: FLPA OR PF0059; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21B(+) KEYWDS STRUCTURAL GENOMICS, FIBRILLARIN, PYROCOCCUS FURIOSUS, SNORNP, KEYWDS 2 RIBOSOMAL RNA PROCESSING, METHYLATION, PFU-65527, PSI, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, SOUTHEAST COLLABORATORY FOR STRUCTURAL KEYWDS 4 GENOMICS, SECSG, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.DENG,N.G.STAROSTINA,Z.-J.LIU,J.P.ROSE,R.M.TERNS,M.P.TERNS,B.- AUTHOR 2 C.WANG,SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS (SECSG) REVDAT 5 14-FEB-24 1PRY 1 SEQADV REVDAT 4 24-JAN-18 1PRY 1 JRNL REVDAT 3 24-FEB-09 1PRY 1 VERSN REVDAT 2 01-FEB-05 1PRY 1 AUTHOR KEYWDS REMARK REVDAT 1 09-MAR-04 1PRY 0 JRNL AUTH L.DENG,N.G.STAROSTINA,Z.-J.LIU,J.P.ROSE,R.M.TERNS,M.P.TERNS, JRNL AUTH 2 B.-C.WANG,SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS JRNL TITL STRUCTURE DETERMINATION OF FIBRILLARIN FROM THE JRNL TITL 2 HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS FURIOSUS JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 315 726 2004 JRNL REFN ISSN 0006-291X JRNL PMID 14975761 JRNL DOI 10.1016/J.BBRC.2004.01.114 REMARK 2 REMARK 2 RESOLUTION. 1.97 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 16201 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) : 0.204 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1749 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 273 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE : 0.4200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 24 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 : 1812 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64000 REMARK 3 B22 (A**2) : 0.48000 REMARK 3 B33 (A**2) : 0.16000 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.23 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) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 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 : 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 : BABINET MODEL WITH MASK 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 : 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 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PRY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-01; 18-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 17-ID; 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.74; 0.97 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18879 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 40.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 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) : 0.05200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 33.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37800 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SINGLE ANOMALOUS REMARK 200 SCATTERING REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, AMMONIUM PHOSPHATE, PH 8.5, REMARK 280 MICROBATCH, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.98350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.68150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.04100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.68150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.98350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.04100 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 49 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 49 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 30 77.36 -119.49 REMARK 500 ARG A 34 56.12 -142.08 REMARK 500 ASP A 184 107.92 -160.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PFU-65527-001 RELATED DB: TARGETDB DBREF 1PRY A 1 227 UNP Q8U4M2 FLPA_PYRFU 1 227 SEQADV 1PRY LEU A 199 UNP Q8U4M2 GLU 199 CONFLICT SEQRES 1 A 227 MET VAL GLU VAL LYS LYS HIS LYS PHE PRO GLY VAL TYR SEQRES 2 A 227 VAL VAL ILE ASP ASP ASP GLY SER GLU LYS 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 HIS ARG SER LYS LEU GLY ALA ALA ILE VAL 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 TYR 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 ILE PRO ILE LEU GLY ASP SEQRES 11 A 227 ALA THR LYS PRO GLU GLU TYR ARG ALA LEU VAL THR 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 LYS ALA 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 LYS GLU SEQRES 16 A 227 VAL GLU ARG LEU 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 PRO FORMUL 2 HOH *158(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 VAL A 141 5 9 HELIX 5 5 THR A 155 TYR A 167 1 13 HELIX 6 6 SER A 180 ASP A 184 1 5 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 O VAL A 14 N LYS A 5 SHEET 3 A 5 GLU A 22 LYS A 27 -1 O ALA A 25 N TYR A 13 SHEET 4 A 5 GLU A 46 ILE A 50 -1 O ARG A 49 N 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 N GLY A 103 O ILE A 127 SHEET 3 B 7 SER A 76 LEU A 80 1 N TYR A 79 O TYR A 102 SHEET 4 B 7 VAL A 144 GLU A 149 1 O PHE A 148 N LEU A 80 SHEET 5 B 7 LEU A 168 LYS A 179 1 O LYS A 169 N 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 208 O VAL A 223 CISPEP 1 GLU A 213 PRO A 214 0 1.98 CRYST1 43.967 62.082 103.363 90.00 90.00 90.00 P 21 21 21 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 0.022744 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016108 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009675 0.00000