HEADER    METAL BINDING PROTEIN                   20-JAN-24   8XZ2              
TITLE     THE STRUCTURAL MODEL OF A HOMODIMERIC D-ALA-D-ALA METALLOPEPTIDASE,   
TITLE    2 VANX, FROM VANCOMYCIN-RESISTANT BACTERIA                             
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: D-ALANYL-D-ALANINE DIPEPTIDASE;                            
COMPND   3 CHAIN: B, C;                                                         
COMPND   4 SYNONYM: D-ALA-D-ALA DIPEPTIDASE,VANCOMYCIN B-TYPE RESISTANCE PROTEIN
COMPND   5 VANX;                                                                
COMPND   6 EC: 3.4.13.22;                                                       
COMPND   7 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECIUM;                           
SOURCE   3 ORGANISM_TAXID: 1352;                                                
SOURCE   4 GENE: VANX;                                                          
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);                       
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   7 EXPRESSION_SYSTEM_VARIANT: PLYSS                                     
KEYWDS    ACID-SELECTIVE UNLABELING, ANTIMICROBIAL RESISTANCE, HOMODIMER,       
KEYWDS   2 RESIDUAL DIPOLAR COUPLING (RDC), TRANSFER CROSS SATURATION (TCS),    
KEYWDS   3 VANCOMYCIN-RESISTANT ENTEROCOCCI, VANX, METAL BINDING PROTEIN        
EXPDTA    SOLUTION NMR                                                          
NUMMDL    4                                                                     
AUTHOR    T.KONUMA,T.TAKAI,C.TSUCHIYA,M.NISHIDA,M.HASHIBA,Y.YAMADA,H.SHIRAI,    
AUTHOR   2 Y.MOTODA,A.NAGADOI,E.CHIKAISHI,K.AKAGI,S.AKASHI,T.YAMAZAKI,H.AKUTSU, 
AUTHOR   3 A.OE,T.IKEGAMI                                                       
REVDAT   1   22-MAY-24 8XZ2    0                                                
JRNL        AUTH   T.KONUMA,T.TAKAI,C.TSUCHIYA,M.NISHIDA,M.HASHIBA,Y.YAMADA,    
JRNL        AUTH 2 H.SHIRAI,Y.MOTODA,A.NAGADOI,E.CHIKAISHI,K.I.AKAGI,S.AKASHI,  
JRNL        AUTH 3 T.YAMAZAKI,H.AKUTSU,T.IKEGAMI                                
JRNL        TITL   ANALYSIS OF THE HOMODIMERIC STRUCTURE OF A D-ALA-D-ALA       
JRNL        TITL 2 METALLOPEPTIDASE, VANX, FROM VANCOMYCIN-RESISTANT BACTERIA.  
JRNL        REF    PROTEIN SCI.                  V.  33 E5002 2024              
JRNL        REFN                   ESSN 1469-896X                               
JRNL        PMID   38723146                                                     
JRNL        DOI    10.1002/PRO.5002                                             
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : HADDOCK 2.4                                          
REMARK   3   AUTHORS     : BONVIN                                               
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: IN TOTAL, 132 RDC-BASED ORIENTATIONAL     
REMARK   3  RESTRAINTS AND SEVEN TCS-BASED INTERSUBUNIT AMBIGUOUS RESTRAINTS    
REMARK   3  WERE IMPOSED IN THE CALCULATIONS. THE LATTER RESTRAINTS INVOLVED    
REMARK   3  RESIDUES IN SEGMENTS B (SELECTED FROM RESIDUES EXHIBITING           
REMARK   3  REMARKABLE TCS EFFECTS) AND C (SELECTED FROM RESIDUES EXHIBITING    
REMARK   3  BOTH REMARKABLE AND MINOR TCS EFFECTS). THESE CONSTRAINTS WERE      
REMARK   3  APPLIED C2-SYMMETRICALLY BETWEEN THE SUBUNITS B AND C IN THE        
REMARK   3  CALCULATIONS.                                                       
REMARK   4                                                                      
REMARK   4 8XZ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-24.                  
REMARK 100 THE DEPOSITION ID IS D_1300043006.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 303                                
REMARK 210  PH                             : 7                                  
REMARK 210  IONIC STRENGTH                 : 50                                 
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : 0.154 MM [U-13C; U-15N; U-2H]      
REMARK 210                                   VANX, 90% H2O/10% D2O              
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 1H/15N TROSY IPAP; TRANSFER        
REMARK 210                                   CROSS SATURATION                   
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ; 500 MHZ                   
REMARK 210  SPECTROMETER MODEL             : AVANCE III HD                      
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : PALES, NMRFAM-SPARKY, NMRPIPE      
REMARK 210   METHOD USED                   : MOLECULAR DYNAMICS                 
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 200                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 4                                  
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: B, C                                  
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 B    57     H    ALA B    58              1.26            
REMARK 500   H    ALA C    57     H    ALA C    58              1.26            
REMARK 500  HD21  ASN C    26     H    THR C    28              1.26            
REMARK 500  HD21  ASN B    26     H    THR B    28              1.27            
REMARK 500  HH22  ARG C   128     OD1  ASP C   130              1.49            
REMARK 500   OD2  ASP B     9    HH21  ARG B    39              1.50            
REMARK 500   OD2  ASP C     9    HH21  ARG C    39              1.51            
REMARK 500   OE2  GLU B   133     HZ3  LYS C    30              1.53            
REMARK 500   HZ2  LYS B    20     OD2  ASP B    25              1.54            
REMARK 500   O    GLY B    69     HD1  HIS B   116              1.57            
REMARK 500   O    GLY C    69     HD1  HIS C   116              1.57            
REMARK 500   OE2  GLU B    10    HH22  ARG B    39              1.57            
REMARK 500   O    GLY C    61     H    LEU C   129              1.58            
REMARK 500   H    THR C     6     O    GLY C    42              1.58            
REMARK 500   HH   TYR B    21     OD2  ASP B   142              1.59            
REMARK 500   HH   TYR B    35     OD1  ASP B    68              1.59            
REMARK 500   HH   TYR C    21     OD2  ASP C   142              1.59            
REMARK 500   HE   ARG C   128     OD2  ASP C   130              1.59            
REMARK 500   HZ2  LYS C    20     OD2  ASP C    25              1.60            
REMARK 500   O    GLY B    61     H    LEU B   129              1.60            
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 HIS B  13      -84.54    -37.49                                   
REMARK 500  1 ARG B  16       68.85   -114.16                                   
REMARK 500  1 ASP B  18       89.88   -161.37                                   
REMARK 500  1 ALA B  19       83.83    -63.31                                   
REMARK 500  1 ASP B  25       53.50    -94.71                                   
REMARK 500  1 GLU B  36      -69.44    -97.52                                   
REMARK 500  1 THR B  59     -146.03    -58.29                                   
REMARK 500  1 TYR B  96       58.05   -156.05                                   
REMARK 500  1 ASN B  98      -20.13     77.08                                   
REMARK 500  1 ILE B 105       48.64    -98.97                                   
REMARK 500  1 SER B 106      -40.71   -158.84                                   
REMARK 500  1 ASN B 194      -15.62     76.54                                   
REMARK 500  1 ASP B 198       29.95   -142.64                                   
REMARK 500  1 HIS C  13      -87.74    -38.16                                   
REMARK 500  1 ARG C  16       70.59   -114.00                                   
REMARK 500  1 ASP C  18       91.96   -164.45                                   
REMARK 500  1 ALA C  19       86.97    -63.03                                   
REMARK 500  1 ASP C  25       52.98    -93.65                                   
REMARK 500  1 VAL C  37      133.76   -170.12                                   
REMARK 500  1 THR C  59     -146.13    -58.19                                   
REMARK 500  1 TYR C  96       57.88   -156.08                                   
REMARK 500  1 ASN C  98      -20.11     76.95                                   
REMARK 500  1 ILE C 105       48.62    -98.97                                   
REMARK 500  1 SER C 106      -40.82   -158.81                                   
REMARK 500  1 ASN C 194      -15.60     76.37                                   
REMARK 500  1 ASP C 198       29.82   -142.78                                   
REMARK 500  2 HIS B  13      -85.57    -37.68                                   
REMARK 500  2 ARG B  16       66.75   -114.70                                   
REMARK 500  2 ASP B  18       90.73   -160.39                                   
REMARK 500  2 ALA B  19      103.21    -57.72                                   
REMARK 500  2 ASP B  25       52.51    -92.94                                   
REMARK 500  2 VAL B  37      139.85   -170.77                                   
REMARK 500  2 THR B  59     -143.03    -57.01                                   
REMARK 500  2 TYR B  96       57.58   -154.52                                   
REMARK 500  2 ASN B  98      -20.77     77.11                                   
REMARK 500  2 ILE B 105       49.10    -99.43                                   
REMARK 500  2 SER B 106      -40.94   -157.92                                   
REMARK 500  2 ASN B 194      -16.88     78.45                                   
REMARK 500  2 ASP B 198       30.26   -143.51                                   
REMARK 500  2 HIS C  13      -83.95    -37.08                                   
REMARK 500  2 ARG C  16       67.36   -116.19                                   
REMARK 500  2 ASP C  18       87.94   -155.85                                   
REMARK 500  2 ASP C  25       52.51    -93.37                                   
REMARK 500  2 VAL C  37      139.73   -172.36                                   
REMARK 500  2 THR C  59     -143.08    -57.05                                   
REMARK 500  2 TYR C  96       57.73   -154.46                                   
REMARK 500  2 ASN C  98      -20.70     77.10                                   
REMARK 500  2 ILE C 105       49.04    -99.45                                   
REMARK 500  2 SER C 106      -40.93   -157.86                                   
REMARK 500  2 ASN C 194      -17.08     78.59                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      96 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 52158   RELATED DB: BMRB                                 
REMARK 900 RELATED ID: 1R44   RELATED DB: PDB                                   
REMARK 900 1R44 IS THE CRYSTAL STRUCTURE OF VANX CONSISTING OF THE SAME AMINO   
REMARK 900 ACID SEQUENCE, DETERMINED BY OTHER AUTHORS.                          
DBREF  8XZ2 B    1   202  UNP    Q06241   VANX_ENTFC       1    202             
DBREF  8XZ2 C    1   202  UNP    Q06241   VANX_ENTFC       1    202             
SEQRES   1 B  202  MET GLU ILE GLY PHE THR PHE LEU ASP GLU ILE VAL HIS          
SEQRES   2 B  202  GLY VAL ARG TRP ASP ALA LYS TYR ALA THR TRP ASP ASN          
SEQRES   3 B  202  PHE THR GLY LYS PRO VAL ASP GLY TYR GLU VAL ASN ARG          
SEQRES   4 B  202  ILE VAL GLY THR TYR GLU LEU ALA GLU SER LEU LEU LYS          
SEQRES   5 B  202  ALA LYS GLU LEU ALA ALA THR GLN GLY TYR GLY LEU LEU          
SEQRES   6 B  202  LEU TRP ASP GLY TYR ARG PRO LYS ARG ALA VAL ASN CYS          
SEQRES   7 B  202  PHE MET GLN TRP ALA ALA GLN PRO GLU ASN ASN LEU THR          
SEQRES   8 B  202  LYS GLU SER TYR TYR PRO ASN ILE ASP ARG THR GLU MET          
SEQRES   9 B  202  ILE SER LYS GLY TYR VAL ALA SER LYS SER SER HIS SER          
SEQRES  10 B  202  ARG GLY SER ALA ILE ASP LEU THR LEU TYR ARG LEU ASP          
SEQRES  11 B  202  THR GLY GLU LEU VAL PRO MET GLY SER ARG PHE ASP PHE          
SEQRES  12 B  202  MET ASP GLU ARG SER HIS HIS ALA ALA ASN GLY ILE SER          
SEQRES  13 B  202  CYS ASN GLU ALA GLN ASN ARG ARG ARG LEU ARG SER ILE          
SEQRES  14 B  202  MET GLU ASN SER GLY PHE GLU ALA TYR SER LEU GLU TRP          
SEQRES  15 B  202  TRP HIS TYR VAL LEU ARG ASP GLU PRO TYR PRO ASN SER          
SEQRES  16 B  202  TYR PHE ASP PHE PRO VAL LYS                                  
SEQRES   1 C  202  MET GLU ILE GLY PHE THR PHE LEU ASP GLU ILE VAL HIS          
SEQRES   2 C  202  GLY VAL ARG TRP ASP ALA LYS TYR ALA THR TRP ASP ASN          
SEQRES   3 C  202  PHE THR GLY LYS PRO VAL ASP GLY TYR GLU VAL ASN ARG          
SEQRES   4 C  202  ILE VAL GLY THR TYR GLU LEU ALA GLU SER LEU LEU LYS          
SEQRES   5 C  202  ALA LYS GLU LEU ALA ALA THR GLN GLY TYR GLY LEU LEU          
SEQRES   6 C  202  LEU TRP ASP GLY TYR ARG PRO LYS ARG ALA VAL ASN CYS          
SEQRES   7 C  202  PHE MET GLN TRP ALA ALA GLN PRO GLU ASN ASN LEU THR          
SEQRES   8 C  202  LYS GLU SER TYR TYR PRO ASN ILE ASP ARG THR GLU MET          
SEQRES   9 C  202  ILE SER LYS GLY TYR VAL ALA SER LYS SER SER HIS SER          
SEQRES  10 C  202  ARG GLY SER ALA ILE ASP LEU THR LEU TYR ARG LEU ASP          
SEQRES  11 C  202  THR GLY GLU LEU VAL PRO MET GLY SER ARG PHE ASP PHE          
SEQRES  12 C  202  MET ASP GLU ARG SER HIS HIS ALA ALA ASN GLY ILE SER          
SEQRES  13 C  202  CYS ASN GLU ALA GLN ASN ARG ARG ARG LEU ARG SER ILE          
SEQRES  14 C  202  MET GLU ASN SER GLY PHE GLU ALA TYR SER LEU GLU TRP          
SEQRES  15 C  202  TRP HIS TYR VAL LEU ARG ASP GLU PRO TYR PRO ASN SER          
SEQRES  16 C  202  TYR PHE ASP PHE PRO VAL LYS                                  
HELIX    1 AA1 ASP B    9  ILE B   11  5                                   3    
HELIX    2 AA2 ALA B   19  THR B   23  5                                   5    
HELIX    3 AA3 TYR B   44  LEU B   56  1                                  13    
HELIX    4 AA4 PRO B   72  ALA B   84  1                                  13    
HELIX    5 AA5 THR B   91  TYR B   96  1                                   6    
HELIX    6 AA6 SER B  114  GLY B  119  5                                   6    
HELIX    7 AA7 ASP B  145  HIS B  149  5                                   5    
HELIX    8 AA8 SER B  156  ASN B  172  1                                  17    
HELIX    9 AA9 ASP C    9  ILE C   11  5                                   3    
HELIX   10 AB1 ALA C   19  THR C   23  5                                   5    
HELIX   11 AB2 TYR C   44  LEU C   56  1                                  13    
HELIX   12 AB3 PRO C   72  ALA C   84  1                                  13    
HELIX   13 AB4 THR C   91  TYR C   96  1                                   6    
HELIX   14 AB5 SER C  114  GLY C  119  5                                   6    
HELIX   15 AB6 ASP C  145  HIS C  149  5                                   5    
HELIX   16 AB7 SER C  156  ASN C  172  1                                  17    
SHEET    1 AA1 2 PHE B   5  PHE B   7  0                                        
SHEET    2 AA1 2 VAL B  41  THR B  43 -1  O  GLY B  42   N  THR B   6           
SHEET    1 AA2 4 TYR B  62  ASP B  68  0                                        
SHEET    2 AA2 4 ALA B 121  ARG B 128 -1  O  ASP B 123   N  TRP B  67           
SHEET    3 AA2 4 HIS B 184  LEU B 187 -1  O  TYR B 185   N  ILE B 122           
SHEET    4 AA2 4 PHE B 175  ALA B 177 -1  N  GLU B 176   O  VAL B 186           
SHEET    1 AA3 2 PHE C   5  PHE C   7  0                                        
SHEET    2 AA3 2 VAL C  41  THR C  43 -1  O  GLY C  42   N  THR C   6           
SHEET    1 AA4 4 TYR C  62  ASP C  68  0                                        
SHEET    2 AA4 4 ALA C 121  ARG C 128 -1  O  ASP C 123   N  TRP C  67           
SHEET    3 AA4 4 HIS C 184  LEU C 187 -1  O  TYR C 185   N  ILE C 122           
SHEET    4 AA4 4 PHE C 175  ALA C 177 -1  N  GLU C 176   O  VAL C 186           
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