HEADER RNA BINDING PROTEIN 22-AUG-07 2R1C TITLE COORDINATES OF THE THERMUS THERMOPHILUS RIBOSOME BINDING FACTOR A TITLE 2 (RBFA) HOMOLOGY MODEL AS FITTED INTO THE CRYO-EM MAP OF A 30S-RBFA TITLE 3 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-BINDING FACTOR A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RBFA, TTHA0907; COMPND 5 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) KEYWDS HELIX-KINK-HELIX, KH DOMAIN, RRNA PROCESSING, RNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.P.DATTA,D.N.WILSON,M.KAWAZOE,N.K.SWAMI,T.KAMINISHI,M.R.SHARMA, AUTHOR 2 T.M.BOOTH,C.TAKEMOTO,P.FUCINI,S.YOKOYAMA,R.K.AGRAWAL REVDAT 6 13-MAR-24 2R1C 1 REMARK REVDAT 5 18-DEC-19 2R1C 1 SOURCE REMARK REVDAT 4 13-JUL-11 2R1C 1 VERSN REVDAT 3 02-FEB-10 2R1C 1 REMARK REVDAT 2 24-FEB-09 2R1C 1 VERSN REVDAT 1 18-MAR-08 2R1C 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. 12.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : O, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1JOS REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : X-RAY COORDINATES OF T. REMARK 3 THERMOPHILUS 30S RIBOSOMAL REMARK 3 SUBUNIT AND THE HOMOLOGY MODEL OF REMARK 3 T. THERMOPHILUS RBFA WERE FITTED REMARK 3 INTO THE 12.5 ANGSTROMS REMARK 3 RESOLUTION CRYO-EM MAP OF THE T. REMARK 3 THERMOPHILUS 30S SUBUNIT-RBFA REMARK 3 COMPLEX. ALL THE ATOMIC REMARK 3 COORDINATES WERE FITTED AS RIGID REMARK 3 BODIES REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--CROSS-CORRELATION BASED MANUAL FITTING REMARK 3 IN O REFINEMENT PROTOCOL--MULTIPLE RIGID BODY REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 12.50 REMARK 3 NUMBER OF PARTICLES : 61207 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV REMARK 3 REMARK 3 OTHER DETAILS: CROSS-CORRELATION COEFFICIENT (CCF) VALUE FOR RBFA REMARK 3 HOMOLOGY MODEL FITTED INTO THE CORRESPONDING CRYO-EM DENSITY WAS REMARK 3 0.79 REMARK 4 REMARK 4 2R1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1000044303. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : THERMUS THERMOPHILUS 30S REMARK 245 RIBOSOMAL SUBUNIT COMPLEXED REMARK 245 WITH RBFA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.03 REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLEY-CRBON FILM REMARK 245 GRID REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID ETHANE REMARK 245 SAMPLE BUFFER : 20MM, HEPES-KOH (PH 7.8), 10MM REMARK 245 MG(OAC)2, 200MM NH4CL, 65MM KCL REMARK 245 PH : 7.80 REMARK 245 SAMPLE DETAILS : RBFA WAS BOUND TO S1-DEPLETED REMARK 245 30S SUBUNIT REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-JAN-05 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 93.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 50760 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : ZEISS IMAGING SCANNER, STEP REMARK 245 SIZE 14MICRO-M REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 465 ALA A 2 REMARK 465 TYR A 3 REMARK 465 GLY A 4 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 ALA A 61 N - CA - CB ANGL. DEV. = 10.1 DEGREES REMARK 500 MET A 79 CG - SD - CE ANGL. DEV. = -9.7 DEGREES REMARK 500 LEU A 82 CB - CG - CD2 ANGL. DEV. = -13.8 DEGREES REMARK 500 TRP A 90 CB - CA - C ANGL. DEV. = -15.1 DEGREES REMARK 500 TRP A 90 CA - CB - CG ANGL. DEV. = 11.4 DEGREES REMARK 500 TRP A 90 CB - CG - CD2 ANGL. DEV. = 10.1 DEGREES REMARK 500 TRP A 90 CB - CG - CD1 ANGL. DEV. = -15.0 DEGREES REMARK 500 TRP A 90 CE2 - CD2 - CG ANGL. DEV. = -5.0 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 ALA A 6 36.28 -77.48 REMARK 500 ALA A 22 -54.95 -4.44 REMARK 500 PHE A 29 -152.02 70.04 REMARK 500 LEU A 59 -85.94 -66.79 REMARK 500 ARG A 91 -90.20 60.89 REMARK 500 ALA A 92 22.45 -30.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 21 ALA A 22 42.67 REMARK 500 ARG A 91 ALA A 92 -57.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 VAL A 49 -17.80 REMARK 500 GLY A 57 -14.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JOS RELATED DB: PDB REMARK 900 RELATED ID: 2DYJ RELATED DB: PDB REMARK 900 RELATED ID: 2R1G RELATED DB: PDB REMARK 900 RELATED ID: EMD-1413 RELATED DB: EMDB DBREF 2R1C A 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 HELIX 1 1 LEU A 8 ILE A 20 1 13 HELIX 2 2 GLU A 55 ALA A 65 1 11 HELIX 3 3 ALA A 65 ARG A 78 1 14 SHEET 1 A 3 LEU A 31 LEU A 38 0 SHEET 2 A 3 VAL A 44 ALA A 51 -1 O GLU A 50 N THR A 32 SHEET 3 A 3 ARG A 84 PRO A 89 1 O GLU A 86 N VAL A 47 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000