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