HEADER    VIRUS                                   17-DEC-20   7DOU              
TITLE     TRIMERIC CEMENT PROTEIN STRUCTURE OF HELICOBACTER PYLORI BACTERIOPHAGE
TITLE    2 KHP40                                                                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: CEMENT PROTEIN GP16;                                       
COMPND   3 CHAIN: 4, 5, 6                                                       
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HELICOBACTER PHAGE KHP40;                       
SOURCE   3 ORGANISM_TAXID: 1204178                                              
KEYWDS    CAPSID, PHAGE, PHAGE HEAD, CRYOEM, VIRUS                              
EXPDTA    ELECTRON MICROSCOPY                                                   
AUTHOR    R.KAMIYA,J.UCHIYAMA,S.MATSUZAKI,K.MURATA,K.IWASAKI,N.MIYAZAKI         
REVDAT   3   05-JUN-24 7DOU    1       REMARK                                   
REVDAT   2   23-FEB-22 7DOU    1       JRNL                                     
REVDAT   1   27-OCT-21 7DOU    0                                                
JRNL        AUTH   R.KAMIYA,J.UCHIYAMA,S.MATSUZAKI,K.MURATA,K.IWASAKI,          
JRNL        AUTH 2 N.MIYAZAKI                                                   
JRNL        TITL   ACID-STABLE CAPSID STRUCTURE OF HELICOBACTER PYLORI          
JRNL        TITL 2 BACTERIOPHAGE KHP30 BY SINGLE-PARTICLE CRYOELECTRON          
JRNL        TITL 3 MICROSCOPY.                                                  
JRNL        REF    STRUCTURE                     V.  30   300 2022              
JRNL        REFN                   ISSN 0969-2126                               
JRNL        PMID   34597601                                                     
JRNL        DOI    10.1016/J.STR.2021.09.001                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    3.00 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   SOFTWARE PACKAGES      : RELION                                    
REMARK   3   RECONSTRUCTION SCHEMA  : NULL                                      
REMARK   3                                                                      
REMARK   3 EM MAP-MODEL FITTING AND REFINEMENT                                  
REMARK   3   PDB ENTRY                    : NULL                                
REMARK   3   REFINEMENT SPACE             : NULL                                
REMARK   3   REFINEMENT PROTOCOL          : NULL                                
REMARK   3   REFINEMENT TARGET            : NULL                                
REMARK   3   OVERALL ANISOTROPIC B VALUE  : NULL                                
REMARK   3                                                                      
REMARK   3 FITTING PROCEDURE : NULL                                             
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)  : 3.000                          
REMARK   3   NUMBER OF PARTICLES               : 6772                           
REMARK   3   CTF CORRECTION METHOD             : PHASE FLIPPING AND AMPLITUDE   
REMARK   3                                       CORRECTION                     
REMARK   3                                                                      
REMARK   3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL                    
REMARK   3                                                                      
REMARK   3 OTHER DETAILS: NULL                                                  
REMARK   4                                                                      
REMARK   4 7DOU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-DEC-20.                  
REMARK 100 THE DEPOSITION ID IS D_1300019860.                                   
REMARK 245                                                                      
REMARK 245 EXPERIMENTAL DETAILS                                                 
REMARK 245   RECONSTRUCTION METHOD          : SINGLE PARTICLE                   
REMARK 245   SPECIMEN TYPE                  : NULL                              
REMARK 245                                                                      
REMARK 245 ELECTRON MICROSCOPE SAMPLE                                           
REMARK 245   SAMPLE TYPE                    : PARTICLE                          
REMARK 245   PARTICLE TYPE                  : POINT                             
REMARK 245   NAME OF SAMPLE                 : HELICOBACTER PHAGE KHP            
REMARK 245   SAMPLE CONCENTRATION (MG ML-1) : NULL                              
REMARK 245   SAMPLE SUPPORT DETAILS         : NULL                              
REMARK 245   SAMPLE VITRIFICATION DETAILS   : NULL                              
REMARK 245   SAMPLE BUFFER                  : NULL                              
REMARK 245   PH                             : 7.20                              
REMARK 245   SAMPLE DETAILS                 : NULL                              
REMARK 245                                                                      
REMARK 245 DATA ACQUISITION                                                     
REMARK 245   DATE OF EXPERIMENT                : NULL                           
REMARK 245   NUMBER OF MICROGRAPHS-IMAGES      : NULL                           
REMARK 245   TEMPERATURE (KELVIN)              : NULL                           
REMARK 245   MICROSCOPE MODEL                  : FEI TITAN KRIOS                
REMARK 245   DETECTOR TYPE                     : FEI FALCON II (4K X 4K)        
REMARK 245   MINIMUM DEFOCUS (NM)              : NULL                           
REMARK 245   MAXIMUM DEFOCUS (NM)              : NULL                           
REMARK 245   MINIMUM TILT ANGLE (DEGREES)      : NULL                           
REMARK 245   MAXIMUM TILT ANGLE (DEGREES)      : NULL                           
REMARK 245   NOMINAL CS                        : NULL                           
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             : NULL                           
REMARK 245   CALIBRATED MAGNIFICATION          : NULL                           
REMARK 245   SOURCE                            : FIELD EMISSION GUN             
REMARK 245   ACCELERATION VOLTAGE (KV)         : 300                            
REMARK 245   IMAGING DETAILS                   : NULL                           
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: TRIMERIC                          
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 4, 5, 6                               
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 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   OE2  GLU 5    40     NZ   LYS 6    79              2.16            
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    THR 4  73       -0.69     67.09                                   
REMARK 500    SER 4  85       -5.15     68.40                                   
REMARK 500    ALA 4  98     -175.45    -66.05                                   
REMARK 500    SER 4 101       -4.85     66.62                                   
REMARK 500    THR 5  73       -0.66     67.10                                   
REMARK 500    SER 5  85       -5.11     68.42                                   
REMARK 500    ALA 5  98     -175.51    -66.01                                   
REMARK 500    SER 5 101       -4.83     66.62                                   
REMARK 500    THR 6  73       -0.65     67.08                                   
REMARK 500    SER 6  85       -5.09     68.40                                   
REMARK 500    ALA 6  98     -175.49    -66.04                                   
REMARK 500    SER 6 101       -4.89     66.63                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: EMD-30778   RELATED DB: EMDB                             
REMARK 900 CAPSID STRUCTURE OF THE CLOSELY RELATED H. PYLORI PHAGE KHP30        
REMARK 900 RELATED ID: EMD-30800   RELATED DB: EMDB                             
REMARK 900 TRIMERIC CEMENT PROTEIN STRUCTURE OF HELICOBACTER PYLORI             
REMARK 900 BACTERIOPHAGE KHP40                                                  
DBREF  7DOU 4    1   124  UNP    I7GUT5   I7GUT5_9CAUD     1    124             
DBREF  7DOU 5    1   124  UNP    I7GUT5   I7GUT5_9CAUD     1    124             
DBREF  7DOU 6    1   124  UNP    I7GUT5   I7GUT5_9CAUD     1    124             
SEQRES   1 4  124  MET LYS GLN LYS VAL HIS SER VAL SER TYR LEU ALA LYS          
SEQRES   2 4  124  ALA GLU PHE GLU TYR LYS ASN GLY VAL TYR ASP LEU VAL          
SEQRES   3 4  124  ALA LEU PRO THR GLY ALA GLU VAL ILE LYS ILE SER LEU          
SEQRES   4 4  124  GLU VAL VAL GLY LEU PRO THR ALA GLY HIS VAL SER VAL          
SEQRES   5 4  124  GLY PHE LYS ASP GLU SER LYS LYS ASN TYR SER SER ILE          
SEQRES   6 4  124  LEU THR LEU PRO VAL ASN GLU THR SER GLY VAL VAL THR          
SEQRES   7 4  124  LYS ASP TYR THR VAL LYS SER ASP LYS ILE VAL ALA ALA          
SEQRES   8 4  124  GLU VAL LYS ASP ALA LEU ALA GLU GLY SER ASP GLY ARG          
SEQRES   9 4  124  PRO VAL LYS CYS VAL LEU ARG ALA LEU TYR PHE LEU PRO          
SEQRES  10 4  124  SER VAL ILE GLU VAL GLU TYR                                  
SEQRES   1 5  124  MET LYS GLN LYS VAL HIS SER VAL SER TYR LEU ALA LYS          
SEQRES   2 5  124  ALA GLU PHE GLU TYR LYS ASN GLY VAL TYR ASP LEU VAL          
SEQRES   3 5  124  ALA LEU PRO THR GLY ALA GLU VAL ILE LYS ILE SER LEU          
SEQRES   4 5  124  GLU VAL VAL GLY LEU PRO THR ALA GLY HIS VAL SER VAL          
SEQRES   5 5  124  GLY PHE LYS ASP GLU SER LYS LYS ASN TYR SER SER ILE          
SEQRES   6 5  124  LEU THR LEU PRO VAL ASN GLU THR SER GLY VAL VAL THR          
SEQRES   7 5  124  LYS ASP TYR THR VAL LYS SER ASP LYS ILE VAL ALA ALA          
SEQRES   8 5  124  GLU VAL LYS ASP ALA LEU ALA GLU GLY SER ASP GLY ARG          
SEQRES   9 5  124  PRO VAL LYS CYS VAL LEU ARG ALA LEU TYR PHE LEU PRO          
SEQRES  10 5  124  SER VAL ILE GLU VAL GLU TYR                                  
SEQRES   1 6  124  MET LYS GLN LYS VAL HIS SER VAL SER TYR LEU ALA LYS          
SEQRES   2 6  124  ALA GLU PHE GLU TYR LYS ASN GLY VAL TYR ASP LEU VAL          
SEQRES   3 6  124  ALA LEU PRO THR GLY ALA GLU VAL ILE LYS ILE SER LEU          
SEQRES   4 6  124  GLU VAL VAL GLY LEU PRO THR ALA GLY HIS VAL SER VAL          
SEQRES   5 6  124  GLY PHE LYS ASP GLU SER LYS LYS ASN TYR SER SER ILE          
SEQRES   6 6  124  LEU THR LEU PRO VAL ASN GLU THR SER GLY VAL VAL THR          
SEQRES   7 6  124  LYS ASP TYR THR VAL LYS SER ASP LYS ILE VAL ALA ALA          
SEQRES   8 6  124  GLU VAL LYS ASP ALA LEU ALA GLU GLY SER ASP GLY ARG          
SEQRES   9 6  124  PRO VAL LYS CYS VAL LEU ARG ALA LEU TYR PHE LEU PRO          
SEQRES  10 6  124  SER VAL ILE GLU VAL GLU TYR                                  
SHEET    1 AA1 6 VAL 4 119  GLU 4 123  0                                        
SHEET    2 AA1 6 LYS 4   2  HIS 4   6 -1  N  VAL 4   5   O  ILE 4 120           
SHEET    3 AA1 6 SER 6   9  PHE 6  16 -1  O  LEU 6  11   N  HIS 4   6           
SHEET    4 AA1 6 LYS 6 107  PHE 6 115 -1  O  TYR 6 114   N  TYR 6  10           
SHEET    5 AA1 6 GLU 6  33  VAL 6  42 -1  N  GLU 6  33   O  PHE 6 115           
SHEET    6 AA1 6 SER 6  74  VAL 6  76 -1  O  GLY 6  75   N  LEU 6  39           
SHEET    1 AA2 6 VAL 4 119  GLU 4 123  0                                        
SHEET    2 AA2 6 LYS 4   2  HIS 4   6 -1  N  VAL 4   5   O  ILE 4 120           
SHEET    3 AA2 6 SER 6   9  PHE 6  16 -1  O  LEU 6  11   N  HIS 4   6           
SHEET    4 AA2 6 LYS 6 107  PHE 6 115 -1  O  TYR 6 114   N  TYR 6  10           
SHEET    5 AA2 6 GLU 6  33  VAL 6  42 -1  N  GLU 6  33   O  PHE 6 115           
SHEET    6 AA2 6 TYR 6  81  THR 6  82 -1  O  TYR 6  81   N  VAL 6  34           
SHEET    1 AA3 4 SER 4   9  PHE 4  16  0                                        
SHEET    2 AA3 4 LYS 4 107  PHE 4 115 -1  O  TYR 4 114   N  TYR 4  10           
SHEET    3 AA3 4 GLU 4  33  VAL 4  42 -1  N  GLU 4  33   O  PHE 4 115           
SHEET    4 AA3 4 SER 4  74  VAL 4  76 -1  O  GLY 4  75   N  LEU 4  39           
SHEET    1 AA4 4 SER 4   9  PHE 4  16  0                                        
SHEET    2 AA4 4 LYS 4 107  PHE 4 115 -1  O  TYR 4 114   N  TYR 4  10           
SHEET    3 AA4 4 GLU 4  33  VAL 4  42 -1  N  GLU 4  33   O  PHE 4 115           
SHEET    4 AA4 4 TYR 4  81  THR 4  82 -1  O  TYR 4  81   N  VAL 4  34           
SHEET    1 AA5 4 GLY 4  21  ALA 4  27  0                                        
SHEET    2 AA5 4 ILE 4  88  ALA 4  96 -1  O  VAL 4  93   N  GLY 4  21           
SHEET    3 AA5 4 GLY 4  48  LYS 4  55 -1  N  LYS 4  55   O  ILE 4  88           
SHEET    4 AA5 4 SER 4  63  PRO 4  69 -1  O  ILE 4  65   N  VAL 4  52           
SHEET    1 AA6 2 LYS 5   2  HIS 5   6  0                                        
SHEET    2 AA6 2 VAL 5 119  GLU 5 123 -1  O  ILE 5 120   N  VAL 5   5           
SHEET    1 AA7 4 SER 5   9  PHE 5  16  0                                        
SHEET    2 AA7 4 LYS 5 107  PHE 5 115 -1  O  TYR 5 114   N  TYR 5  10           
SHEET    3 AA7 4 GLU 5  33  VAL 5  42 -1  N  GLU 5  33   O  PHE 5 115           
SHEET    4 AA7 4 SER 5  74  VAL 5  76 -1  O  GLY 5  75   N  LEU 5  39           
SHEET    1 AA8 4 SER 5   9  PHE 5  16  0                                        
SHEET    2 AA8 4 LYS 5 107  PHE 5 115 -1  O  TYR 5 114   N  TYR 5  10           
SHEET    3 AA8 4 GLU 5  33  VAL 5  42 -1  N  GLU 5  33   O  PHE 5 115           
SHEET    4 AA8 4 TYR 5  81  THR 5  82 -1  O  TYR 5  81   N  VAL 5  34           
SHEET    1 AA9 4 GLY 5  21  ALA 5  27  0                                        
SHEET    2 AA9 4 ILE 5  88  ALA 5  96 -1  O  VAL 5  93   N  GLY 5  21           
SHEET    3 AA9 4 GLY 5  48  LYS 5  55 -1  N  LYS 5  55   O  ILE 5  88           
SHEET    4 AA9 4 SER 5  63  PRO 5  69 -1  O  ILE 5  65   N  VAL 5  52           
SHEET    1 AB1 2 LYS 6   2  HIS 6   6  0                                        
SHEET    2 AB1 2 VAL 6 119  GLU 6 123 -1  O  ILE 6 120   N  VAL 6   5           
SHEET    1 AB2 4 GLY 6  21  ALA 6  27  0                                        
SHEET    2 AB2 4 ILE 6  88  ALA 6  96 -1  O  VAL 6  93   N  GLY 6  21           
SHEET    3 AB2 4 GLY 6  48  LYS 6  55 -1  N  LYS 6  55   O  ILE 6  88           
SHEET    4 AB2 4 SER 6  63  PRO 6  69 -1  O  ILE 6  65   N  VAL 6  52           
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 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