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Database: PDB
Entry: 2JN0
LinkDB: 2JN0
Original site: 2JN0 
HEADER    MEMBRANE PROTEIN                        15-DEC-06   2JN0              
TITLE     SOLUTION NMR STRUCTURE OF THE YGDR PROTEIN FROM ESCHERICHIA COLI.     
TITLE    2 NORTHEAST STRUCTURAL GENOMICS TARGET ER382A.                         
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: HYPOTHETICAL LIPOPROTEIN YGDR;                             
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: HYPOTHETICAL LIPOPROTEIN YGDR, RESIDUES 2-53;              
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;                               
SOURCE   3 ORGANISM_TAXID: 562;                                                 
SOURCE   4 GENE: YGDR;                                                          
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC;                          
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;                               
SOURCE   9 EXPRESSION_SYSTEM_VECTOR: ER382A-21.2                                
KEYWDS    SOLUTION NMR STRUCTURE, HYPOTHETICAL LIPOPROTEIN, PSI-2 TARGET,       
KEYWDS   2 STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, NORTHEAST         
KEYWDS   3 STRUCTURAL GENOMICS CONSORTIUM, NESG, MEMBRANE PROTEIN               
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    P.ROSSI,C.X.CHEN,M.JIANG,K.CUNNINGHAM,L.MA,R.XIAO,J.C.LIU,M.BARAN,    
AUTHOR   2 G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST STRUCTURAL    
AUTHOR   3 GENOMICS CONSORTIUM (NESG)                                           
REVDAT   3   05-FEB-20 2JN0    1       REMARK SEQADV                            
REVDAT   2   24-FEB-09 2JN0    1       VERSN                                    
REVDAT   1   01-MAY-07 2JN0    0                                                
JRNL        AUTH   P.ROSSI,C.X.CHEN,M.JIANG,K.CUNNINGHAM,L.MA,R.XIAO,J.LIU,     
JRNL        AUTH 2 M.C.BARAN,G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE       
JRNL        TITL   SOLUTION NMR STRUCTURE OF THE YGDR PROTEIN FROM ESCHERICHIA  
JRNL        TITL 2 COLI. NORTHEAST STRUCTURAL GENOMICS TARGET ER382A.           
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNSSOLVE 1.1, X-PLOR 2.11.2, PROCHECK NMR 3.51,      
REMARK   3                 MOLPROBITY 3.01, QUEEN 1.1, PSVS 1.3                 
REMARK   3   AUTHORS     : BRUNGER, ET. AL. (CNSSOLVE), CLORE ET. AL. (X        
REMARK   3                 -PLOR), LASKOWSKI, MACARTHUR (PROCHECK NMR),         
REMARK   3                 LOVELL, RICHARDSON ET. AL. (MOLPROBITY), NABUURS,    
REMARK   3                 VUISTER (QUEEN), BHATTACHARYA, MONTELIONE (PSVS)     
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NOESY ASSIGNMENT MADE WITH ITERATIVE      
REMARK   3  METHOD USING CNS, HYPER (DIHEDRAL) AND DYANA FOLLOWED BY NIH-       
REMARK   3  XPLOR FOR SIMMULATED ANNEALING MD. CONVERGED STRUCTURES WERE        
REMARK   3  FURTHER MINIMIZED USING CNS IN EXPLICIT H2O SHELL (NILGES           
REMARK   3  PROTOCOL). FULL LENGTH SEQUENCE WAS CARRIED THROUGH THE             
REMARK   3  REFINEMENT PROTOCOL. COORDINATES FROM DISORDERED REGIONS,           
REMARK   3  INCLUDING HEXHIS TAG, WERE NOT REPORTED. STRUCTURE IS BASED ON      
REMARK   3  439 CONSTRAINTS (216 LONG RANGE), 43 DIHEDRAL AND 20 H-BOND.        
REMARK   4                                                                      
REMARK   4 2JN0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-DEC-06.                  
REMARK 100 THE DEPOSITION ID IS D_1000100036.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 293                                
REMARK 210  PH                             : 6.5                                
REMARK 210  IONIC STRENGTH                 : 0.1                                
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 1.17 MM [U-100% 13C; U-100% 15N]   
REMARK 210                                   ER382A, 10 MM DTT, 5 MM CACL2,     
REMARK 210                                   0.1 M NACL, 20 MM MES, 0.02 %      
REMARK 210                                   SODIUM AZIDE                       
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D 1H-13C HSQC;    
REMARK 210                                   3D HNCO; 3D HNCACB; 3D HBHA(CO)    
REMARK 210                                   NH; 3D 1H-15N NOESY; 3D 1H-13C     
REMARK 210                                   NOESY; 3D HCCH-TOCSY; 3D HN(COCA)  
REMARK 210                                   CB; 3D HCCH-COSY; 3D CCH-TOCSY     
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : AVANCE                             
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : AUTOSTRUCTURE 2.1.1, NMRPIPE,      
REMARK 210                                   SPARKY, MOLMOL, CNS, PROCHECK,     
REMARK 210                                   XPLOR-NIH, DIANA, QUEEN 1.1        
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  : TARGET FUNCTION                    
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY.   
REMARK 210  MONOMER IN SOLUTION BY NMR TC = 8.2 +/- 1.0 NS (1D T1/T1RHO +/-     
REMARK 210  FIT STD). POSSIBLE CIS PEPTIDE RES. 20K-21P. COULD NOT BE           
REMARK 210  ANAMBIGUOSLY ESTABLISHED DUE TO SPECTRAL OVERLAP. COORDINATES       
REMARK 210  REPORTED FROM RESIDUE 4 TO 53 SECTION BASED ON ORDER PARAMETER.     
REMARK 210  MANUAL RESONANCE ASSIGNMENT. 13C AND 15N EDITED NOESY WERE WERE     
REMARK 210  ASSIGNED USING AUTOSTRUCTURE. DIHEDRAL ANGLE RESTRAINTS             
REMARK 210  DETERMINED BY HYPER AND TALOS. ASSIGNMENT STATS (EXCLUDING C-       
REMARK 210  TERM TAG): BACKBONE 80.4%, SIDECHAIN 77.7%, AROMATIC (SC) 100%,     
REMARK 210  VL METHYL STEREOSP. 80%. STRUCTURE QUALITY FACTOR PSVS 1.3:         
REMARK 210  ORDERED RESIDUES RANGES B-STRAND (14-16, 6-9, 47-49, 22-24, 29-     
REMARK 210  33, 39-43, 65, 50-51, 56-57) [S(PHI)+S(PSI)]>1.8. RMSD 0.6 BB,      
REMARK 210  1.1 ALL HEAVY ATOMS. RAMA: 84.1% MOST FAV, 13.6% ADDTL.ALL.,2.2%    
REMARK 210  GEN. ALL.,0.1% DISALL. PROCHECK (PSI-PHI): 0.75/-2.64 (RAW/Z),      
REMARK 210  PROCHECK (ALL): -0.6/-3.55 (RAW/Z), MOLPROBITY CLASH: 23.61/-       
REMARK 210  2.53 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY        
REMARK 210  PEAKLISTS TO STRUCTURE): RECALL: 0.925, PRECISION: 0.916, F-        
REMARK 210  MEASURE: 0.921, DP-SCORE: 0.731. MONOMER BY LIGHT SCATTERING        
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: 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;                   
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                            
REMARK 465   MODELS 1-20                                                        
REMARK 465     RES C SSSEQI                                                     
REMARK 465     MET A     1                                                      
REMARK 465     SER A     2                                                      
REMARK 465     SER A     3                                                      
REMARK 465     LEU A    54                                                      
REMARK 465     GLU A    55                                                      
REMARK 465     HIS A    56                                                      
REMARK 465     HIS A    57                                                      
REMARK 465     HIS A    58                                                      
REMARK 465     HIS A    59                                                      
REMARK 465     HIS A    60                                                      
REMARK 465     HIS A    61                                                      
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                                                                      
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 THR A  27      -35.52   -137.74                                   
REMARK 500  1 SER A  48      -72.40   -105.94                                   
REMARK 500  2 VAL A   6      139.32   -172.74                                   
REMARK 500  2 LYS A  20       52.29    170.31                                   
REMARK 500  2 SER A  48      -64.70    -92.58                                   
REMARK 500  2 ILE A  51      117.55     71.19                                   
REMARK 500  3 TYR A   5     -158.12   -142.16                                   
REMARK 500  3 VAL A   6      177.92     62.35                                   
REMARK 500  3 LYS A  20       78.44     71.63                                   
REMARK 500  3 ILE A  50      -32.64   -173.15                                   
REMARK 500  3 ILE A  51       99.76     65.23                                   
REMARK 500  4 LYS A  20      132.76     77.13                                   
REMARK 500  4 ILE A  51       14.74   -144.72                                   
REMARK 500  5 LYS A  20       78.45     72.63                                   
REMARK 500  5 SER A  48      -63.66    -93.08                                   
REMARK 500  5 ILE A  50      -74.28   -130.69                                   
REMARK 500  6 LYS A  20       79.70     72.95                                   
REMARK 500  6 SER A  48      -64.29    -99.63                                   
REMARK 500  6 ILE A  50      -77.23   -112.64                                   
REMARK 500  7 VAL A   6      132.67   -175.95                                   
REMARK 500  7 LYS A  20       76.69     92.83                                   
REMARK 500  7 SER A  48      -62.41   -152.56                                   
REMARK 500  7 GLU A  52      -74.33    -52.83                                   
REMARK 500  8 LYS A  20       78.46     72.71                                   
REMARK 500  8 SER A  48      -73.46   -128.71                                   
REMARK 500  8 GLU A  52      -93.02     61.61                                   
REMARK 500  9 VAL A   6       83.71     39.35                                   
REMARK 500  9 LYS A  20       85.98    162.52                                   
REMARK 500  9 SER A  48      -61.53   -126.92                                   
REMARK 500  9 ILE A  50      -57.11   -134.94                                   
REMARK 500  9 GLU A  52      -70.69    -57.01                                   
REMARK 500 10 TYR A   5       -8.12   -168.76                                   
REMARK 500 10 LYS A  20       95.42     79.49                                   
REMARK 500 10 SER A  48      -66.83   -137.21                                   
REMARK 500 11 LYS A  20       76.98     91.61                                   
REMARK 500 11 SER A  48      -78.11   -109.01                                   
REMARK 500 12 VAL A   6      159.07     70.46                                   
REMARK 500 12 ASP A  11       29.55    -76.76                                   
REMARK 500 12 LYS A  20       65.62    157.86                                   
REMARK 500 13 VAL A   6      120.17     73.14                                   
REMARK 500 13 LYS A  10      -59.81    -28.12                                   
REMARK 500 13 LYS A  20       75.10     67.78                                   
REMARK 500 13 SER A  48      -68.88    -91.11                                   
REMARK 500 13 GLN A  49      147.85   -179.49                                   
REMARK 500 13 GLU A  52       49.62    -87.00                                   
REMARK 500 14 TYR A   5      112.22   -160.50                                   
REMARK 500 14 VAL A   6      154.82     65.43                                   
REMARK 500 14 LYS A  20       73.49     69.46                                   
REMARK 500 14 SER A  48      -65.49   -130.80                                   
REMARK 500 15 LYS A  20       71.52     71.94                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      71 RAMACHANDRAN OUTLIERS.                        
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 GLY A   19     LYS A   20          4       140.99                    
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 15079   RELATED DB: BMRB                                 
REMARK 900 RELATED ID: ER382A   RELATED DB: TARGETDB                            
DBREF  2JN0 A    2    53  UNP    P65294   YGDR_ECOLI      21     72             
SEQADV 2JN0 MET A    1  UNP  P65294              CLONING ARTIFACT               
SEQADV 2JN0 LEU A   54  UNP  P65294              CLONING ARTIFACT               
SEQADV 2JN0 GLU A   55  UNP  P65294              CLONING ARTIFACT               
SEQADV 2JN0 HIS A   56  UNP  P65294              EXPRESSION TAG                 
SEQADV 2JN0 HIS A   57  UNP  P65294              EXPRESSION TAG                 
SEQADV 2JN0 HIS A   58  UNP  P65294              EXPRESSION TAG                 
SEQADV 2JN0 HIS A   59  UNP  P65294              EXPRESSION TAG                 
SEQADV 2JN0 HIS A   60  UNP  P65294              EXPRESSION TAG                 
SEQADV 2JN0 HIS A   61  UNP  P65294              EXPRESSION TAG                 
SEQRES   1 A   61  MET SER SER ASP TYR VAL MET ALA THR LYS ASP GLY ARG          
SEQRES   2 A   61  MET ILE LEU THR ASP GLY LYS PRO GLU ILE ASP ASP ASP          
SEQRES   3 A   61  THR GLY LEU VAL SER TYR HIS ASP GLN GLN GLY ASN ALA          
SEQRES   4 A   61  MET GLN ILE ASN ARG ASP ASP VAL SER GLN ILE ILE GLU          
SEQRES   5 A   61  ARG LEU GLU HIS HIS HIS HIS HIS HIS                          
SHEET    1   A 3 MET A  14  LEU A  16  0                                        
SHEET    2   A 3 VAL A   6  THR A   9 -1  N  MET A   7   O  ILE A  15           
SHEET    3   A 3 VAL A  47  GLN A  49 -1  O  GLN A  49   N  ALA A   8           
SHEET    1   B 3 GLU A  22  ILE A  23  0                                        
SHEET    2   B 3 LEU A  29  HIS A  33 -1  O  SER A  31   N  GLU A  22           
SHEET    3   B 3 ALA A  39  ASN A  43 -1  O  MET A  40   N  TYR A  32           
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                                                                  
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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