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Database: PDB
Entry: 1YNA
LinkDB: 1YNA
Original site: 1YNA 
HEADER    HYDROLASE                               22-AUG-96   1YNA              
TITLE     ENDO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.0                      
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: ENDO-1,4-BETA-XYLANASE;                                    
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: XYNA;                                                       
COMPND   5 EC: 3.2.1.8                                                          
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: THERMOMYCES LANUGINOSUS;                        
SOURCE   3 ORGANISM_TAXID: 5541;                                                
SOURCE   4 STRAIN: TSIKLINSKY;                                                  
SOURCE   5 ATCC: DSM 5826                                                       
KEYWDS    HYDROLASE, XYLANASE                                                   
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    K.GRUBER,C.KRATKY                                                     
REVDAT   4   07-MAR-18 1YNA    1       REMARK                                   
REVDAT   3   24-FEB-09 1YNA    1       VERSN                                    
REVDAT   2   09-JUL-99 1YNA    1       JRNL                                     
REVDAT   1   12-FEB-97 1YNA    0                                                
JRNL        AUTH   K.GRUBER,G.KLINTSCHAR,M.HAYN,A.SCHLACHER,W.STEINER,C.KRATKY  
JRNL        TITL   THERMOPHILIC XYLANASE FROM THERMOMYCES LANUGINOSUS:          
JRNL        TITL 2 HIGH-RESOLUTION X-RAY STRUCTURE AND MODELING STUDIES.        
JRNL        REF    BIOCHEMISTRY                  V.  37 13475 1998              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   9753433                                                      
JRNL        DOI    10.1021/BI980864L                                            
REMARK   1                                                                      
REMARK   1 REFERENCE 1                                                          
REMARK   1  AUTH   A.SCHLACHER,K.HOLZMANN,M.HAYN,W.STEINER,H.SCHWAB             
REMARK   1  TITL   THREE-DIMENSIONAL STRUCTURE OF ENDO-1,4-BETA-XYLANASE II     
REMARK   1  TITL 2 FROM TRICHODERMA REESEI: TWO CONFORMATIONAL STATES IN THE    
REMARK   1  TITL 3 ACTIVE SITE                                                  
REMARK   1  REF    J.BIOTECHNOL.                 V.  49   211 1996              
REMARK   1  REFN                   ISSN 0168-1656                               
REMARK   1 REFERENCE 2                                                          
REMARK   1  AUTH   A.TORRONEN,A.HARKKI,J.ROUVINEN                               
REMARK   1  TITL   THREE-DIMENSIONAL STRUCTURE OF ENDO-1,4-BETA-XYLANASE II     
REMARK   1  TITL 2 FROM TRICHODERMA REESEI: TWO CONFORMATIONAL STATES IN THE    
REMARK   1  TITL 3 ACTIVE SITE                                                  
REMARK   1  REF    EMBO J.                       V.  13  2493 1994              
REMARK   1  REFN                   ISSN 0261-4189                               
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.55 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : SHELXL-93                                            
REMARK   3   AUTHORS     : G.M.SHELDRICK                                        
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 25.30                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 83.9                           
REMARK   3   CROSS-VALIDATION METHOD           : NULL                           
REMARK   3   FREE R VALUE TEST SET SELECTION   : NULL                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).                         
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL                   
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.193                  
REMARK   3   FREE R VALUE                  (NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 26211                  
REMARK   3                                                                      
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).                     
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : NULL                   
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : 0.155                  
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 19452                  
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS      : 1512                                          
REMARK   3   NUCLEIC ACID ATOMS : 0                                             
REMARK   3   HETEROGEN ATOMS    : 0                                             
REMARK   3   SOLVENT ATOMS      : 138                                           
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : 1650.0                  
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : 0.00                    
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : 0                       
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : 6598                    
REMARK   3   NUMBER OF RESTRAINTS                     : 6091                    
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : 0.008                   
REMARK   3   ANGLE DISTANCES                      (A) : 1.400                   
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL                    
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL                    
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : NULL                    
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : NULL                    
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : NULL                    
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : NULL                    
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : NULL                    
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : NULL                    
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED: BABINET'S PRINCIPLE (SWAT)                            
REMARK   3                                                                      
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER                        
REMARK   3   SPECIAL CASE: NULL                                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1YNA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.                                
REMARK 100 THE DEPOSITION ID IS D_1000177412.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 24-APR-95                          
REMARK 200  TEMPERATURE           (KELVIN) : 298                                
REMARK 200  PH                             : 4.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                     
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : SIEMENS                            
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418                             
REMARK 200  MONOCHROMATOR                  : GRAPHITE(002)                      
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : NULL                               
REMARK 200  DETECTOR MANUFACTURER          : SIEMENS                            
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : CCP4, XDS                          
REMARK 200  DATA SCALING SOFTWARE          : XDS, CCP4                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 26211                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.550                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 25.300                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 83.9                               
REMARK 200  DATA REDUNDANCY                : 3.100                              
REMARK 200  R MERGE                    (I) : 0.07500                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 7.7000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.59                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 30.7                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.35400                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: NULL                                           
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: SHELXL-93, X-PLOR 3.1                                 
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 51.00                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 5-10% PEG-4000, PH 4.0, T=4 DEG C,       
REMARK 280  TEMPERATURE 277K                                                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,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        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000       26.28500            
REMARK 290   SMTRY3   2  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 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    TYR A 171     -138.45   -100.80                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: PLANAR GROUPS                                              
REMARK 500                                                                      
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL                 
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE                    
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN                    
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS                        
REMARK 500 AN RMSD GREATER THAN THIS VALUE                                      
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        RMS     TYPE                                    
REMARK 500    ARG A  81         0.08    SIDE CHAIN                              
REMARK 500    ARG A 116         0.12    SIDE CHAIN                              
REMARK 500    ARG A 122         0.20    SIDE CHAIN                              
REMARK 500    ARG A 161         0.20    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  1YNA A    2   194  UNP    O43097   XYNA_THELA      33    225             
SEQRES   1 A  194  PCA THR THR PRO ASN SER GLU GLY TRP HIS ASP GLY TYR          
SEQRES   2 A  194  TYR TYR SER TRP TRP SER ASP GLY GLY ALA GLN ALA THR          
SEQRES   3 A  194  TYR THR ASN LEU GLU GLY GLY THR TYR GLU ILE SER TRP          
SEQRES   4 A  194  GLY ASP GLY GLY ASN LEU VAL GLY GLY LYS GLY TRP ASN          
SEQRES   5 A  194  PRO GLY LEU ASN ALA ARG ALA ILE HIS PHE GLU GLY VAL          
SEQRES   6 A  194  TYR GLN PRO ASN GLY ASN SER TYR LEU ALA VAL TYR GLY          
SEQRES   7 A  194  TRP THR ARG ASN PRO LEU VAL GLU TYR TYR ILE VAL GLU          
SEQRES   8 A  194  ASN PHE GLY THR TYR ASP PRO SER SER GLY ALA THR ASP          
SEQRES   9 A  194  LEU GLY THR VAL GLU CYS ASP GLY SER ILE TYR ARG LEU          
SEQRES  10 A  194  GLY LYS THR THR ARG VAL ASN ALA PRO SER ILE ASP GLY          
SEQRES  11 A  194  THR GLN THR PHE ASP GLN TYR TRP SER VAL ARG GLN ASP          
SEQRES  12 A  194  LYS ARG THR SER GLY THR VAL GLN THR GLY CYS HIS PHE          
SEQRES  13 A  194  ASP ALA TRP ALA ARG ALA GLY LEU ASN VAL ASN GLY ASP          
SEQRES  14 A  194  HIS TYR TYR GLN ILE VAL ALA THR GLU GLY TYR PHE SER          
SEQRES  15 A  194  SER GLY TYR ALA ARG ILE THR VAL ALA ASP VAL GLY              
MODRES 1YNA PCA A    1  GLU  PYROGLUTAMIC ACID                                  
HET    PCA  A   1       8                                                       
HETNAM     PCA PYROGLUTAMIC ACID                                                
FORMUL   1  PCA    C5 H7 N O3                                                   
FORMUL   2  HOH   *138(H2 O)                                                    
HELIX    1   1 GLY A  153  ALA A  162  1                                  10    
SHEET    1   A 5 ALA A  25  LEU A  30  0                                        
SHEET    2   A 5 TYR A  35  TRP A  39 -1  N  SER A  38   O  THR A  26           
SHEET    3   A 5 SER A 183  ALA A 191 -1  N  ILE A 188   O  TYR A  35           
SHEET    4   A 5 ALA A  59  GLN A  67 -1  N  HIS A  61   O  ALA A 191           
SHEET    5   A 5 GLY A 148  GLN A 151 -1  N  VAL A 150   O  ILE A  60           
SHEET    1   B 9 SER A   6  HIS A  10  0                                        
SHEET    2   B 9 TYR A  13  SER A  19 -1  N  TRP A  17   O  SER A   6           
SHEET    3   B 9 ASN A  44  TRP A  51 -1  N  GLY A  50   O  TYR A  14           
SHEET    4   B 9 TYR A 172  TYR A 180 -1  N  GLY A 179   O  LEU A  45           
SHEET    5   B 9 SER A  72  THR A  80 -1  N  TYR A  77   O  ILE A 174           
SHEET    6   B 9 VAL A  85  GLY A  94 -1  N  ASN A  92   O  LEU A  74           
SHEET    7   B 9 PHE A 134  GLN A 142  1  N  ASP A 135   O  GLU A  86           
SHEET    8   B 9 SER A 113  ARG A 122 -1  N  ARG A 122   O  PHE A 134           
SHEET    9   B 9 THR A 103  CYS A 110 -1  N  CYS A 110   O  SER A 113           
SSBOND   1 CYS A  110    CYS A  154                          1555   1555  2.03  
LINK         C   PCA A   1                 N   THR A   2     1555   1555  1.34  
CISPEP   1 ASN A   52    PRO A   53          0         6.67                     
CISPEP   2 ASN A   82    PRO A   83          0         2.68                     
CRYST1   40.960   52.570   50.470  90.00 100.43  90.00 P 1 21 1      2          
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      0.024414  0.000000  0.004494        0.00000                         
SCALE2      0.000000  0.019022  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.020147        0.00000                         
HETATM    1  N   PCA A   1     -17.564   4.471  29.286  1.00 61.06           N  
HETATM    2  CA  PCA A   1     -16.876   3.328  29.863  1.00 57.40           C  
HETATM    3  CB  PCA A   1     -18.014   2.278  29.801  1.00 60.21           C  
HETATM    4  CG  PCA A   1     -19.305   3.108  30.000  1.00 62.17           C  
HETATM    5  CD  PCA A   1     -18.905   4.391  29.332  1.00 63.25           C  
HETATM    6  OE  PCA A   1     -19.697   5.218  28.909  1.00 70.21           O  
HETATM    7  C   PCA A   1     -15.719   2.929  28.980  1.00 49.53           C  
HETATM    8  O   PCA A   1     -15.290   3.731  28.166  1.00 55.15           O  
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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