HEADER RIBOSOMAL PROTEIN 14-SEP-06 2DYJ
TITLE CRYSTAL STRUCTURE OF RIBOSOME-BINDING FACTOR A FROM THERMUS
TITLE 2 THERMOPHILUS HB8
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RIBOSOME-BINDING FACTOR A;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS;
SOURCE 3 ORGANISM_TAXID: 300852;
SOURCE 4 STRAIN: HB8;
SOURCE 5 GENE: TTHA0907;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11B
KEYWDS 16S RRNA PROCESSING, 17S RNA, KH DOMAIN, STRUCTURAL GENOMICS, NPPSFA,
KEYWDS 2 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES,
KEYWDS 3 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, RIBOSOMAL
KEYWDS 4 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR M.KAWAZOE,C.TAKEMOTO,R.NAKAYAMA-USHIKOSHI,T.TERADA,M.SHIROUZU,
AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 5 25-OCT-23 2DYJ 1 REMARK
REVDAT 4 13-JUL-11 2DYJ 1 VERSN
REVDAT 3 24-FEB-09 2DYJ 1 VERSN
REVDAT 2 18-MAR-08 2DYJ 1 JRNL HEADER
REVDAT 1 14-MAR-07 2DYJ 0
JRNL AUTH P.P.DATTA,D.N.WILSON,M.KAWAZOE,N.K.SWAMI,T.KAMINISHI,
JRNL AUTH 2 M.R.SHARMA,T.M.BOOTH,C.TAKEMOTO,P.FUCINI,S.YOKOYAMA,
JRNL AUTH 3 R.K.AGRAWAL
JRNL TITL STRUCTURAL ASPECTS OF RBFA ACTION DURING SMALL RIBOSOMAL
JRNL TITL 2 SUBUNIT ASSEMBLY.
JRNL REF MOL.CELL V. 28 434 2007
JRNL REFN ISSN 1097-2765
JRNL PMID 17996707
JRNL DOI 10.1016/J.MOLCEL.2007.08.026
REMARK 2
REMARK 2 RESOLUTION. 1.84 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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.92
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 591976.420
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 13793
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) : 0.199
REMARK 3 FREE R VALUE : 0.245
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 700
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009
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) : 1.84
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2164
REMARK 3 BIN R VALUE (WORKING SET) : 0.2490
REMARK 3 BIN FREE R VALUE : 0.3230
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 128
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1467
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 105
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 16.60
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 3.49000
REMARK 3 B22 (A**2) : -5.75000
REMARK 3 B33 (A**2) : 2.25000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -4.31000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21
REMARK 3 ESD FROM SIGMAA (A) : 0.17
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) : 0.28
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27
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) : 21.50
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790
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) : 3.050 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.750 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 4.990 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.000 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.37
REMARK 3 BSOL : 51.02
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 2DYJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-SEP-06.
REMARK 100 THE DEPOSITION ID IS D_1000026002.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-MAY-06
REMARK 200 TEMPERATURE (KELVIN) : 90
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : PHOTON FACTORY
REMARK 200 BEAMLINE : BL-5A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13813
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840
REMARK 200 RESOLUTION RANGE LOW (A) : 43.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 3.730
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.06100
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.70
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.31200
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.220
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 1JOS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 33.36
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M AMMONIUM DIHYDROGEN PHOSPHATE,
REMARK 280 0.08M TRIS-HCL PH8.5, 9.6% V/V GLYCEROL ANHYDROUS, 0.02M BIS-
REMARK 280 TRIS PROPANE PH 7.0, 0.08M MAGNESIUM FORMATE, VAPOR DIFFUSION,
REMARK 280 SITTING DROP, TEMPERATURE 293K
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 32.91900
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
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 ALA A 2
REMARK 465 TYR A 3
REMARK 465 ALA A 95
REMARK 465 MET B 1
REMARK 465 ALA B 2
REMARK 465 SER B 93
REMARK 465 PRO B 94
REMARK 465 ALA B 95
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 GLU A 54 77.59 32.60
REMARK 500 ARG B 91 -15.89 -48.45
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: TTK003000788.2 RELATED DB: TARGETDB
DBREF 2DYJ A 1 95 UNP Q5SJV1 Q5SJV1_THET8 1 95
DBREF 2DYJ B 1 95 UNP Q5SJV1 Q5SJV1_THET8 1 95
SEQRES 1 A 95 MET ALA TYR GLY LYS ALA HIS LEU GLU ALA GLN LEU LYS
SEQRES 2 A 95 ARG ALA LEU ALA GLU GLU ILE GLN ALA LEU GLU ASP PRO
SEQRES 3 A 95 ARG LEU PHE LEU LEU THR VAL GLU ALA VAL ARG LEU SER
SEQRES 4 A 95 LYS ASP GLY SER VAL LEU SER VAL TYR VAL GLU ALA PHE
SEQRES 5 A 95 ARG GLU GLU GLU GLY ALA LEU ARG ALA LEU SER ARG ALA
SEQRES 6 A 95 GLU ARG ARG LEU VAL ALA ALA LEU ALA ARG ARG VAL ARG
SEQRES 7 A 95 MET ARG ARG LEU PRO ARG LEU GLU PHE LEU PRO TRP ARG
SEQRES 8 A 95 ALA SER PRO ALA
SEQRES 1 B 95 MET ALA TYR GLY LYS ALA HIS LEU GLU ALA GLN LEU LYS
SEQRES 2 B 95 ARG ALA LEU ALA GLU GLU ILE GLN ALA LEU GLU ASP PRO
SEQRES 3 B 95 ARG LEU PHE LEU LEU THR VAL GLU ALA VAL ARG LEU SER
SEQRES 4 B 95 LYS ASP GLY SER VAL LEU SER VAL TYR VAL GLU ALA PHE
SEQRES 5 B 95 ARG GLU GLU GLU GLY ALA LEU ARG ALA LEU SER ARG ALA
SEQRES 6 B 95 GLU ARG ARG LEU VAL ALA ALA LEU ALA ARG ARG VAL ARG
SEQRES 7 B 95 MET ARG ARG LEU PRO ARG LEU GLU PHE LEU PRO TRP ARG
SEQRES 8 B 95 ALA SER PRO ALA
FORMUL 3 HOH *105(H2 O)
HELIX 1 1 GLY A 4 ALA A 22 1 19
HELIX 2 2 ASP A 25 PHE A 29 5 5
HELIX 3 3 GLU A 54 ALA A 65 1 12
HELIX 4 4 ALA A 65 ARG A 75 1 11
HELIX 5 5 ARG A 91 SER A 93 5 3
HELIX 6 6 GLY B 4 ALA B 22 1 19
HELIX 7 7 LEU B 23 GLU B 24 5 2
HELIX 8 8 ASP B 25 PHE B 29 5 5
HELIX 9 9 GLU B 54 ALA B 65 1 12
HELIX 10 10 ALA B 65 VAL B 77 1 13
SHEET 1 A 3 THR A 32 LEU A 38 0
SHEET 2 A 3 VAL A 44 GLU A 50 -1 O SER A 46 N ARG A 37
SHEET 3 A 3 ARG A 84 PRO A 89 1 O GLU A 86 N VAL A 47
SHEET 1 B 3 THR B 32 LEU B 38 0
SHEET 2 B 3 VAL B 44 GLU B 50 -1 O GLU B 50 N THR B 32
SHEET 3 B 3 ARG B 84 PRO B 89 1 O GLU B 86 N VAL B 47
CRYST1 28.426 65.838 43.173 90.00 96.18 90.00 P 1 21 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 0.035179 0.000000 0.003810 0.00000
SCALE2 0.000000 0.015189 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023298 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
