HEADER RIBOSOME 08-NOV-99 1DD5 TITLE CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTOR, TITLE 2 RRF COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME RECYCLING FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS THREE-HELIX BUNDLE, BETA-ALPHA-BETA SANDWICH, RIBOSOME EXPDTA X-RAY DIFFRACTION AUTHOR M.SELMER,S.AL-KARADAGHI,G.HIROKAWA,A.KAJI,A.LILJAS REVDAT 5 07-FEB-24 1DD5 1 REMARK REVDAT 4 07-MAR-18 1DD5 1 REMARK REVDAT 3 24-FEB-09 1DD5 1 VERSN REVDAT 2 27-NOV-02 1DD5 1 JRNL REMARK REVDAT 1 22-DEC-99 1DD5 0 JRNL AUTH M.SELMER,S.AL-KARADAGHI,G.HIROKAWA,A.KAJI,A.LILJAS JRNL TITL CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING JRNL TITL 2 FACTOR: A TRNA MIMIC. JRNL REF SCIENCE V. 286 2349 1999 JRNL REFN ISSN 0036-8075 JRNL PMID 10600747 JRNL DOI 10.1126/SCIENCE.286.5448.2349 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.SELMER,S.AL-KARADAGHI,G.HIROKAWA,A.KAJI,A.LILJAS REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF THERMOTOGA REMARK 1 TITL 2 MARITIMA RIBOSOME RECYCLING FACTOR REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 2049 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444999012494 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.ATARASHI,A.KAJI REMARK 1 TITL CLONING AND OVEREXPRESSION OF THERMOTOGA MARITIMA RRF REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 11878 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 : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 597 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1808 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 100 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1504 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.35 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.820 ; 0.750 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.360 ; 1.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 11.210; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 13.180; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 23.60 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SOLVED BY SELENOMETHIONINE MAD REMARK 4 REMARK 4 1DD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000009986. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-99; 13-JAN-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0; 100.0 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; MAX II REMARK 200 BEAMLINE : BM14; I711 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786,0.9788,0.9184; 0.947 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11648 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.15300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, ACETATE, GLYCEROL , REMARK 280 PH 5.5, VAPOR DIFFUSION, TEMPERATURE 298K 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 148.77500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.62500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 223.16250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.62500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.62500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.38750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.62500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.62500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 223.16250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.62500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.62500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.38750 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 148.77500 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 238 LIES ON A SPECIAL POSITION. 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: 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 ASN A 52 -8.86 -57.55 REMARK 500 SER A 60 -101.55 -100.92 REMARK 500 GLU A 62 -19.50 -31.22 REMARK 500 LYS A 72 -14.97 -47.28 REMARK 500 ASN A 96 -53.86 -123.89 REMARK 500 GLU A 184 38.51 -72.40 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 ACY A 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 281 DBREF 1DD5 A 1 185 UNP Q9X1B9 RRF_THEMA 1 185 SEQRES 1 A 185 MET VAL ASN PRO PHE ILE LYS GLU ALA LYS GLU LYS MET SEQRES 2 A 185 LYS ARG THR LEU GLU LYS ILE GLU ASP GLU LEU ARG LYS SEQRES 3 A 185 MET ARG THR GLY LYS PRO SER PRO ALA ILE LEU GLU GLU SEQRES 4 A 185 ILE LYS VAL ASP TYR TYR GLY VAL PRO THR PRO VAL ASN SEQRES 5 A 185 GLN LEU ALA THR ILE SER ILE SER GLU GLU ARG THR LEU SEQRES 6 A 185 VAL ILE LYS PRO TRP ASP LYS SER VAL LEU SER LEU ILE SEQRES 7 A 185 GLU LYS ALA ILE ASN ALA SER ASP LEU GLY LEU ASN PRO SEQRES 8 A 185 ILE ASN ASP GLY ASN VAL ILE ARG LEU VAL PHE PRO SER SEQRES 9 A 185 PRO THR THR GLU GLN ARG GLU LYS TRP VAL LYS LYS ALA SEQRES 10 A 185 LYS GLU ILE VAL GLU GLU GLY LYS ILE ALA ILE ARG ASN SEQRES 11 A 185 ILE ARG ARG GLU ILE LEU LYS LYS ILE LYS GLU ASP GLN SEQRES 12 A 185 LYS GLU GLY LEU ILE PRO GLU ASP ASP ALA LYS ARG LEU SEQRES 13 A 185 GLU ASN GLU ILE GLN LYS LEU THR ASP GLU PHE ILE GLU SEQRES 14 A 185 LYS LEU ASP GLU VAL PHE GLU ILE LYS LYS GLU GLU ILE SEQRES 15 A 185 MET GLU PHE HET ACY A 280 4 HET ACY A 281 4 HETNAM ACY ACETIC ACID FORMUL 2 ACY 2(C2 H4 O2) FORMUL 4 HOH *65(H2 O) HELIX 1 1 ASN A 3 MET A 27 1 25 HELIX 2 2 SER A 33 GLU A 38 5 6 HELIX 3 3 SER A 73 SER A 85 1 13 HELIX 4 4 THR A 106 GLU A 145 1 40 HELIX 5 5 PRO A 149 GLU A 184 1 36 SHEET 1 A 2 LYS A 41 TYR A 44 0 SHEET 2 A 2 VAL A 47 PRO A 50 -1 N VAL A 47 O TYR A 44 SHEET 1 B 4 ALA A 55 ILE A 59 0 SHEET 2 B 4 THR A 64 PRO A 69 -1 N VAL A 66 O SER A 58 SHEET 3 B 4 ILE A 98 VAL A 101 -1 N ILE A 98 O ILE A 67 SHEET 4 B 4 ILE A 92 ASN A 93 -1 O ILE A 92 N ARG A 99 SITE 1 AC1 2 ARG A 132 HOH A 244 SITE 1 AC2 2 LYS A 68 ASN A 96 CRYST1 47.250 47.250 297.550 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 0.021164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021164 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003361 0.00000