PDB Short entry for 6U5G
HEADER    ISOMERASE                               27-AUG-19   6U5G              
TITLE     MICROED STRUCTURE OF A FIB-MILLED CYPA CRYSTAL                        
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A;                     
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: PPIASE A,CYCLOPHILIN A,CYCLOSPORIN A-BINDING PROTEIN,       
COMPND   5 ROTAMASE A;                                                          
COMPND   6 EC: 5.2.1.8;                                                         
COMPND   7 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: PPIA, CYPA;                                                    
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);                       
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008                                      
KEYWDS    PEPTIDYL-PROLYL, CIS-TRANS, ISOMERASE, CYCLOPHILIN                    
EXPDTA    ELECTRON CRYSTALLOGRAPHY                                              
AUTHOR    A.M.WOLFF,M.W.MARTYNOWYCZ,W.ZHAO,T.GONEN,J.S.FRASER,M.C.THOMPSON      
REVDAT   3   11-MAR-20 6U5G    1       JRNL                                     
REVDAT   2   12-FEB-20 6U5G    1       AUTHOR JRNL                              
REVDAT   1   29-JAN-20 6U5G    0                                                
JRNL        AUTH   A.M.WOLFF,I.D.YOUNG,R.G.SIERRA,A.S.BREWSTER,M.W.MARTYNOWYCZ, 
JRNL        AUTH 2 E.NANGO,M.SUGAHARA,T.NAKANE,K.ITO,A.AQUILA,A.BHOWMICK,       
JRNL        AUTH 3 J.T.BIEL,S.CARBAJO,A.E.COHEN,S.CORTEZ,A.GONZALEZ,T.HINO,     
JRNL        AUTH 4 D.IM,J.D.KORALEK,M.KUBO,T.S.LAZAROU,T.NOMURA,S.OWADA,        
JRNL        AUTH 5 A.SAMELSON,T.TANAKA,R.TANAKA,E.M.THOMPSON,H.VAN DEN BEDEM,   
JRNL        AUTH 6 R.A.WOLDEYES,F.YUMOTO,W.ZHAO,K.TONO,S.BOUTET,S.IWATA,        
JRNL        AUTH 7 T.GONEN,N.K.SAUTER,J.S.FRASER,M.C.THOMPSON                   
JRNL        TITL   COMPARING SERIAL X-RAY CRYSTALLOGRAPHY AND MICROCRYSTAL      
JRNL        TITL 2 ELECTRON DIFFRACTION (MICROED) AS METHODS FOR ROUTINE        
JRNL        TITL 3 STRUCTURE DETERMINATION FROM SMALL MACROMOLECULAR CRYSTALS   
JRNL        REF    IUCRJ                         V.   7   306 2020              
JRNL        REFN                   ESSN 2052-2525                               
JRNL        DOI    10.1107/S205225252000072X                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.50 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.16_3549                                     
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : NULL                                          
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 26.48                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 86.0                           
REMARK   3   NUMBER OF REFLECTIONS             : 11440                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.187                           
REMARK   3   R VALUE            (WORKING SET) : 0.185                           
REMARK   3   FREE R VALUE                     : 0.224                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 3.460                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 396                             
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 26.4800 -  3.6000    0.84     3582   122  0.1461 0.1548        
REMARK   3     2  3.6000 -  2.8600    0.87     3717   141  0.2033 0.2848        
REMARK   3     3  2.8600 -  2.5000    0.87     3745   133  0.2665 0.3217        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.422            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.539           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 35.52                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 30.60                          
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  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.011           1276                                  
REMARK   3   ANGLE     :  0.732           1711                                  
REMARK   3   CHIRALITY :  0.055            177                                  
REMARK   3   PLANARITY :  0.005            226                                  
REMARK   3   DIHEDRAL  : 12.819            744                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 6U5G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-19.                  
REMARK 100 THE DEPOSITION ID IS D_1000243874.                                   
REMARK 240                                                                      
REMARK 240 EXPERIMENTAL DETAILS                                                 
REMARK 240   RECONSTRUCTION METHOD          : CRYSTALLOGRAPHY                   
REMARK 240   SAMPLE TYPE                    : 3D ARRAY                          
REMARK 240   SPECIMEN TYPE                  : NULL                              
REMARK 240 DATA ACQUISITION                                                     
REMARK 240   DATE OF DATA COLLECTION        : NULL                              
REMARK 240   TEMPERATURE           (KELVIN) : NULL                              
REMARK 240   PH                             : NULL                              
REMARK 240   NUMBER OF CRYSTALS USED        : NULL                              
REMARK 240   MICROSCOPE MODEL               : FEI TALOS ARCTICA                 
REMARK 240   DETECTOR TYPE                  : TVIPS TEMCAM-F416 (4K X 4K)       
REMARK 240   ACCELERATION VOLTAGE (KV)      : 200                               
REMARK 240   NUMBER OF UNIQUE REFLECTIONS   : NULL                              
REMARK 240   RESOLUTION RANGE HIGH      (A) : NULL                              
REMARK 240   RESOLUTION RANGE LOW       (A) : NULL                              
REMARK 240   DATA SCALING SOFTWARE          : XDS                               
REMARK 240   COMPLETENESS FOR RANGE     (%) : NULL                              
REMARK 240   DATA REDUNDANCY                : NULL                              
REMARK 240 IN THE HIGHEST RESOLUTION SHELL                                      
REMARK 240   HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL                     
REMARK 240   HIGHEST RESOLUTION SHELL, RANGE LOW  (A) :NULL                     
REMARK 240   COMPLETENESS FOR SHELL     (%) : NULL                              
REMARK 240   DATA REDUNDANCY IN SHELL       : NULL                              
REMARK 240   R MERGE FOR SHELL          (I) : NULL                              
REMARK 240   METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT      
REMARK 240   SOFTWARE USED                  : PHASER                            
REMARK 240   STARTING MODEL                 : PDB ENTRY 4YUM                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
REMARK 290       4555   X+1/2,-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       21.20000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       43.88000            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       26.70000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       43.88000            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       21.20000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       26.70000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
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 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     GLU A   165                                                      
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  HD22  ASN A    35     O    HOH A   206              1.51            
REMARK 500   O    ASP A   123     O    HOH A   201              2.18            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)               
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   RES CSSEQI ATM2   DEVIATION                     
REMARK 500    CYS A 161   CB    CYS A 161   SG     -0.162                       
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    PHE A  60      -76.24   -131.72                                   
REMARK 500    HIS A  70       16.25     56.51                                   
REMARK 500    THR A 107       26.32   -142.07                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: EMD-20645   RELATED DB: EMDB                             
REMARK 900 MICROED STRUCTURE OF A FIB-MILLED CYPA CRYSTAL                       
DBREF  6U5G A    1   165  UNP    P62937   PPIA_HUMAN       1    165             
SEQRES   1 A  165  MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP          
SEQRES   2 A  165  GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA          
SEQRES   3 A  165  ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU          
SEQRES   4 A  165  SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS          
SEQRES   5 A  165  PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY          
SEQRES   6 A  165  ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE          
SEQRES   7 A  165  TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS          
SEQRES   8 A  165  HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY          
SEQRES   9 A  165  PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA          
SEQRES  10 A  165  LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY          
SEQRES  11 A  165  LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU          
SEQRES  12 A  165  ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE          
SEQRES  13 A  165  THR ILE ALA ASP CYS GLY GLN LEU GLU                          
FORMUL   2  HOH   *32(H2 O)                                                     
HELIX    1 AA1 VAL A   29  GLY A   42  1                                  14    
HELIX    2 AA2 THR A  119  ASP A  123  5                                   5    
HELIX    3 AA3 GLY A  135  ARG A  144  1                                  10    
SHEET    1 AA1 8 ARG A  55  ILE A  57  0                                        
SHEET    2 AA1 8 MET A  61  GLY A  64 -1  O  GLN A  63   N  ARG A  55           
SHEET    3 AA1 8 PHE A 112  CYS A 115 -1  O  ILE A 114   N  CYS A  62           
SHEET    4 AA1 8 ILE A  97  MET A 100 -1  N  SER A  99   O  PHE A 113           
SHEET    5 AA1 8 VAL A 128  GLU A 134 -1  O  GLY A 130   N  LEU A  98           
SHEET    6 AA1 8 GLU A  15  LEU A  24 -1  N  SER A  21   O  LYS A 133           
SHEET    7 AA1 8 THR A   5  VAL A  12 -1  N  PHE A   8   O  VAL A  20           
SHEET    8 AA1 8 ILE A 156  GLN A 163 -1  O  ASP A 160   N  ASP A   9           
CRYST1   42.400   53.400   87.760  90.00  90.00  90.00 P 21 21 21    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      0.023585  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.018727  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.011395        0.00000