HEADER    DNA BINDING PROTEIN/DNA                 21-SEP-20   7D3W              
TITLE     NON-SPECIFIC AND SPECIFIC INTERACTIONS WORK COOPERATIVELY TO PROMOTE  
TITLE    2 CYTIDINE DEAMINATION CATALYZED BY APOBEC3A                           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA DC->DU-EDITING ENZYME APOBEC-3A;                       
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: A3A,PHORBOLIN-1;                                            
COMPND   5 EC: 3.5.4.38;                                                        
COMPND   6 ENGINEERED: YES;                                                     
COMPND   7 MUTATION: YES;                                                       
COMPND   8 MOL_ID: 2;                                                           
COMPND   9 MOLECULE: DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*TP*T)-3');              
COMPND  10 CHAIN: B;                                                            
COMPND  11 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: APOBEC3A;                                                      
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 MOL_ID: 2;                                                           
SOURCE   9 SYNTHETIC: YES;                                                      
SOURCE  10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;                            
SOURCE  11 ORGANISM_TAXID: 32630                                                
KEYWDS    DNA BINDING PROTEIN-DNA COMPLEX                                       
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    C.CAO,Y.LIU,W.LAN                                                     
REVDAT   4   15-MAY-24 7D3W    1       REMARK                                   
REVDAT   3   14-JUN-23 7D3W    1       REMARK                                   
REVDAT   2   20-APR-22 7D3W    1       AUTHOR JRNL                              
REVDAT   1   06-OCT-21 7D3W    0                                                
JRNL        AUTH   Y.LIU,W.LAN,C.WANG,C.CAO                                     
JRNL        TITL   TWO DIFFERENT KINDS OF INTERACTION MODES OF DEAMINASE        
JRNL        TITL 2 APOBEC3A WITH SINGLE-STRANDED DNA IN SOLUTION DETECTED BY    
JRNL        TITL 3 NUCLEAR MAGNETIC RESONANCE.                                  
JRNL        REF    PROTEIN SCI.                  V.  31   443 2022              
JRNL        REFN                   ESSN 1469-896X                               
JRNL        PMID   34792260                                                     
JRNL        DOI    10.1002/PRO.4242                                             
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
REMARK   3   AUTHORS     : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ         
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 7D3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-SEP-20.                  
REMARK 100 THE DEPOSITION ID IS D_1300018651.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 293                                
REMARK 210  PH                             : 7.3                                
REMARK 210  IONIC STRENGTH                 : 375                                
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : 25 MM SODIUM PHOSPHATE, 200 MM     
REMARK 210                                   SODIUM CHLORIDE, 50 UM ZINC        
REMARK 210                                   CHLORIDE, 5 MM DTT, 0.28 MM [U-    
REMARK 210                                   13C; U-15N] A3A, 0.56 MM DNA, 90%  
REMARK 210                                   H2O/10% D2O; 25 MM SODIUM          
REMARK 210                                   PHOSPHATE, 200 MM SODIUM           
REMARK 210                                   CHLORIDE, 50 UM ZINC CHLORIDE, 5   
REMARK 210                                   MM DTT, 0.28 MM [U-13C; U-15N]     
REMARK 210                                   A3A, 0.56 MM DNA, 100% D2O         
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 3D HNCO; 3D HNCACB; 3D HN(CO)CA;   
REMARK 210                                   3D CBCA(CO)NH; 3D 1H-15N NOESY;    
REMARK 210                                   3D 1H-15N TOCSY; 2D 1H-15N HSQC;   
REMARK 210                                   2D 1H-13C HSQC; 3D 1H-13C NOESY    
REMARK 210                                   ALIPHATIC; 3D 1H-13C NOESY         
REMARK 210                                   AROMATIC; 3D HCCH-TOCSY; 2D        
REMARK 210                                   FILTER TOCSY; 2D FILTER NOESY;     
REMARK 210                                   3D 15N-FILTER-EDIT NOESY; 3D 13C-  
REMARK 210                                   FILTER-EDIT NOESY                  
REMARK 210  SPECTROMETER FIELD STRENGTH    : 900 MHZ; 800 MHZ                   
REMARK 210  SPECTROMETER MODEL             : AVANCE; DD2                        
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER; AGILENT                    
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRDRAW, SPARKY, X-PLOR NIH        
REMARK 210   METHOD USED                   : SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST         
REMARK 210                                   ENERGY                             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: NULL                                                         
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
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: DIMERIC                           
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
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   H    ALA A    59     HH   TYR A    67              1.31            
REMARK 500   O    LEU A   179     H    SER A   183              1.50            
REMARK 500   O    CYS A   161     H    PHE A   165              1.59            
REMARK 500   O    HIS A   182     H    LEU A   186              1.60            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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  3  DT B 202   C6  -  C5  -  C7  ANGL. DEV. =  -3.6 DEGREES          
REMARK 500  4  DT B 202   C6  -  C5  -  C7  ANGL. DEV. =  -3.6 DEGREES          
REMARK 500  5  DT B 208   C6  -  C5  -  C7  ANGL. DEV. =  -3.6 DEGREES          
REMARK 500  7  DT B 202   C6  -  C5  -  C7  ANGL. DEV. =  -3.7 DEGREES          
REMARK 500  9  DT B 202   C6  -  C5  -  C7  ANGL. DEV. =  -3.7 DEGREES          
REMARK 500 12  DT B 202   C6  -  C5  -  C7  ANGL. DEV. =  -3.7 DEGREES          
REMARK 500 13  DT B 201   C6  -  C5  -  C7  ANGL. DEV. =  -3.7 DEGREES          
REMARK 500 13  DT B 202   C6  -  C5  -  C7  ANGL. DEV. =  -3.6 DEGREES          
REMARK 500 13  DT B 209   C6  -  C5  -  C7  ANGL. DEV. =  -3.6 DEGREES          
REMARK 500 14  DT B 202   C6  -  C5  -  C7  ANGL. DEV. =  -3.7 DEGREES          
REMARK 500 17  DT B 202   C6  -  C5  -  C7  ANGL. DEV. =  -3.6 DEGREES          
REMARK 500 17  DT B 208   C6  -  C5  -  C7  ANGL. DEV. =  -3.6 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  1 ALA A   3     -178.99     48.10                                   
REMARK 500  1 GLN A  50       93.35    177.29                                   
REMARK 500  1 ASN A  61       77.45    168.43                                   
REMARK 500  1 ARG A  69     -139.30    -81.57                                   
REMARK 500  1 CYS A 101       94.58   -162.73                                   
REMARK 500  1 SER A 103      142.49    171.28                                   
REMARK 500  1 TYR A 130       89.17   -173.10                                   
REMARK 500  1 ASP A 131      -39.87   -147.06                                   
REMARK 500  1 ASP A 133     -178.12    -56.89                                   
REMARK 500  1 ALA A 148       32.04    -65.51                                   
REMARK 500  2 ALA A   3      140.05    175.97                                   
REMARK 500  2 HIS A  11        7.75    -62.10                                   
REMARK 500  2 GLN A  50       87.17    178.13                                   
REMARK 500  2 ASN A  61       77.94    170.05                                   
REMARK 500  2 CYS A 101       80.46   -174.11                                   
REMARK 500  2 SER A 103     -157.72   -168.80                                   
REMARK 500  2 TYR A 130       89.80   -169.23                                   
REMARK 500  2 ASP A 131      -43.57   -147.31                                   
REMARK 500  2 ALA A 148       31.59    -63.65                                   
REMARK 500  3 MET A  48     -165.91    -57.10                                   
REMARK 500  3 GLN A  50       65.40   -177.36                                   
REMARK 500  3 ASN A  61       76.47    168.45                                   
REMARK 500  3 CYS A 101      113.97   -162.01                                   
REMARK 500  3 SER A 103      156.52    170.60                                   
REMARK 500  3 TYR A 130      112.70   -173.40                                   
REMARK 500  3 ASP A 131      -44.26   -145.95                                   
REMARK 500  3 ASP A 133      169.67    -39.91                                   
REMARK 500  3 PRO A 134       -4.79    -51.35                                   
REMARK 500  3 ALA A 148       32.81    -66.09                                   
REMARK 500  4 HIS A  29      -57.08   -128.24                                   
REMARK 500  4 LYS A  30      103.08     50.74                                   
REMARK 500  4 MET A  48     -172.36    -69.38                                   
REMARK 500  4 GLN A  50       88.97   -163.38                                   
REMARK 500  4 ASN A  61       76.54    167.61                                   
REMARK 500  4 CYS A 101      103.18   -167.06                                   
REMARK 500  4 TYR A 130       88.22   -171.81                                   
REMARK 500  4 ASP A 131      -42.01   -148.16                                   
REMARK 500  4 ALA A 148       31.62    -63.20                                   
REMARK 500  4 ASP A 167       69.12   -118.83                                   
REMARK 500  5 ASN A  23       -6.23    -59.21                                   
REMARK 500  5 GLN A  50       85.99   -172.67                                   
REMARK 500  5 ASN A  61       75.70    166.47                                   
REMARK 500  5 CYS A 101       14.37   -161.88                                   
REMARK 500  5 SER A 103     -135.70   -155.94                                   
REMARK 500  5 TYR A 130       98.34   -170.82                                   
REMARK 500  5 ASP A 131      -41.35   -146.72                                   
REMARK 500  5 PRO A 134      -86.22    -82.94                                   
REMARK 500  5 ALA A 148       32.43    -64.50                                   
REMARK 500  6 MET A  48     -163.78    -69.95                                   
REMARK 500  6 GLN A  50       93.62   -170.10                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     187 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A 201  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HIS A  70   ND1                                                    
REMARK 620 2 CYS A 101   SG  107.3                                              
REMARK 620 3 CYS A 106   SG  108.8 108.0                                        
REMARK 620 N                    1     2                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 36388   RELATED DB: BMRB                                 
REMARK 900 NON-SPECIFIC AND SPECIFIC INTERACTIONS WORK COOPERATIVELY TO         
REMARK 900 PROMOTE CYTIDINE DEAMINATION CATALYZED BY APOBEC3A                   
DBREF  7D3W A    1   199  UNP    P31941   ABC3A_HUMAN      1    199             
DBREF  7D3W B  200   209  PDB    7D3W     7D3W           200    209             
SEQADV 7D3W ASN A   63  UNP  P31941    LEU    63 ENGINEERED MUTATION            
SEQADV 7D3W SER A   64  UNP  P31941    CYS    64 ENGINEERED MUTATION            
SEQADV 7D3W GLN A   72  UNP  P31941    GLU    72 ENGINEERED MUTATION            
SEQADV 7D3W GLN A  171  UNP  P31941    CYS   171 ENGINEERED MUTATION            
SEQRES   1 A  199  MET GLU ALA SER PRO ALA SER GLY PRO ARG HIS LEU MET          
SEQRES   2 A  199  ASP PRO HIS ILE PHE THR SER ASN PHE ASN ASN GLY ILE          
SEQRES   3 A  199  GLY ARG HIS LYS THR TYR LEU CYS TYR GLU VAL GLU ARG          
SEQRES   4 A  199  LEU ASP ASN GLY THR SER VAL LYS MET ASP GLN HIS ARG          
SEQRES   5 A  199  GLY PHE LEU HIS ASN GLN ALA LYS ASN LEU ASN SER GLY          
SEQRES   6 A  199  PHE TYR GLY ARG HIS ALA GLN LEU ARG PHE LEU ASP LEU          
SEQRES   7 A  199  VAL PRO SER LEU GLN LEU ASP PRO ALA GLN ILE TYR ARG          
SEQRES   8 A  199  VAL THR TRP PHE ILE SER TRP SER PRO CYS PHE SER TRP          
SEQRES   9 A  199  GLY CYS ALA GLY GLU VAL ARG ALA PHE LEU GLN GLU ASN          
SEQRES  10 A  199  THR HIS VAL ARG LEU ARG ILE PHE ALA ALA ARG ILE TYR          
SEQRES  11 A  199  ASP TYR ASP PRO LEU TYR LYS GLU ALA LEU GLN MET LEU          
SEQRES  12 A  199  ARG ASP ALA GLY ALA GLN VAL SER ILE MET THR TYR ASP          
SEQRES  13 A  199  GLU PHE LYS HIS CYS TRP ASP THR PHE VAL ASP HIS GLN          
SEQRES  14 A  199  GLY GLN PRO PHE GLN PRO TRP ASP GLY LEU ASP GLU HIS          
SEQRES  15 A  199  SER GLN ALA LEU SER GLY ARG LEU ARG ALA ILE LEU GLN          
SEQRES  16 A  199  ASN GLN GLY ASN                                              
SEQRES   1 B   10   DA  DT  DT  DT  DT  DC  DA  DA  DT  DT                      
HET     ZN  A 201       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   3   ZN    ZN 2+                                                        
HELIX    1 AA1 ASP A   14  ASN A   24  1                                  11    
HELIX    2 AA2 HIS A   70  GLN A   83  1                                  14    
HELIX    3 AA3 GLY A  105  ASN A  117  1                                  13    
HELIX    4 AA4 LEU A  135  GLY A  147  1                                  13    
HELIX    5 AA5 THR A  154  VAL A  166  1                                  13    
HELIX    6 AA6 GLY A  178  ASN A  196  1                                  19    
SHEET    1 AA1 3 THR A  44  LYS A  47  0                                        
SHEET    2 AA1 3 TYR A  32  ASP A  41 -1  N  ARG A  39   O  VAL A  46           
SHEET    3 AA1 3 GLY A  53  HIS A  56 -1  O  LEU A  55   N  LEU A  33           
SHEET    1 AA2 5 THR A  44  LYS A  47  0                                        
SHEET    2 AA2 5 TYR A  32  ASP A  41 -1  N  ARG A  39   O  VAL A  46           
SHEET    3 AA2 5 TYR A  90  TRP A  98 -1  O  PHE A  95   N  CYS A  34           
SHEET    4 AA2 5 ARG A 121  ARG A 128  1  O  ARG A 123   N  TRP A  94           
SHEET    5 AA2 5 VAL A 150  ILE A 152  1  O  SER A 151   N  ILE A 124           
LINK         ND1 HIS A  70                ZN    ZN A 201     1555   1555  2.00  
LINK         SG  CYS A 101                ZN    ZN A 201     1555   1555  2.30  
LINK         SG  CYS A 106                ZN    ZN A 201     1555   1555  2.31  
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                         
MODEL        1