HEADER    HYDROLASE                               03-JAN-24   8RLF              
TITLE     HYDROGENATED HEN EGG-WHITE LYSOZYME AT ROOM TEMPERATURE               
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: LYSOZYME C;                                                
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV;            
COMPND   5 EC: 3.2.1.17                                                         
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;                                  
SOURCE   3 ORGANISM_COMMON: CHICKEN;                                            
SOURCE   4 ORGANISM_TAXID: 9031                                                 
KEYWDS    LYSOZYME, HYDROGENATED, ROOM TEMPERATURE, HYDROLASE                   
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.RAMOS,V.LAUX,S.A.MASON,M.LEMEE,M.BOWLER,K.DIEDERICHS,M.HAERTLEIN,   
AUTHOR   2 V.T.FORSYTH,E.MOSSOU,S.LARSEN,A.E.LANGKILDE                          
REVDAT   2   29-JAN-25 8RLF    1       JRNL                                     
REVDAT   1   06-NOV-24 8RLF    0                                                
JRNL        AUTH   J.RAMOS,V.LAUX,S.A.MASON,M.H.LEMEE,M.W.BOWLER,K.DIEDERICHS,  
JRNL        AUTH 2 M.HAERTLEIN,V.T.FORSYTH,E.MOSSOU,S.LARSEN,A.E.LANGKILDE      
JRNL        TITL   STRUCTURE AND DYNAMICS OF THE ACTIVE SITE OF HEN EGG-WHITE   
JRNL        TITL 2 LYSOZYME FROM ATOMIC RESOLUTION NEUTRON CRYSTALLOGRAPHY.     
JRNL        REF    STRUCTURE                     V.  33   136 2025              
JRNL        REFN                   ISSN 0969-2126                               
JRNL        PMID   39577430                                                     
JRNL        DOI    10.1016/J.STR.2024.10.030                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    0.96 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : SHELX                                                
REMARK   3   AUTHORS     : G.M.SHELDRICK                                        
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 0.96                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 21.67                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL                           
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.8                           
REMARK   3   CROSS-VALIDATION METHOD           : FREE R-VALUE                   
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM                         
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) : NULL                   
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) : NULL                   
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)) : NULL                   
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)) : NULL                   
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS      : 1001                                          
REMARK   3   NUCLEIC ACID ATOMS : 0                                             
REMARK   3   HETEROGEN ATOMS    : 40                                            
REMARK   3   SOLVENT ATOMS      : 108                                           
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : NULL                    
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : NULL                    
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL                    
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : NULL                    
REMARK   3   NUMBER OF RESTRAINTS                     : NULL                    
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : NULL                    
REMARK   3   ANGLE DISTANCES                      (A) : NULL                    
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: NULL                                                  
REMARK   3                                                                      
REMARK   3  STEREOCHEMISTRY TARGET VALUES : NULL                                
REMARK   3   SPECIAL CASE: NULL                                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 8RLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JAN-24.                  
REMARK 100 THE DEPOSITION ID IS D_1292133897.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 21-SEP-16                          
REMARK 200  TEMPERATURE           (KELVIN) : 298                                
REMARK 200  PH                             : 4.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : ESRF                               
REMARK 200  BEAMLINE                       : ID29                               
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.688                              
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS 6M                 
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : XSCALE                             
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 61660                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 0.960                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 21.670                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.8                               
REMARK 200  DATA REDUNDANCY                : 6.600                              
REMARK 200  R MERGE                    (I) : 0.12100                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 16.5000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.96                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 0.99                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 99.5                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 5.70                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.48100                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 4.700                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHENIX                                                
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 32.41                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 2 % NANO3, 0.1 M NA ACETATE PH 4.5,      
REMARK 280  BATCH MODE, TEMPERATURE 291K                                        
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1                              
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,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                                                                      
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 1390 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 6890 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 KCAL/MOL                          
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: 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    ARG A   5   NE  -  CZ  -  NH1 ANGL. DEV. =   3.7 DEGREES          
REMARK 500    ARG A  14   NH1 -  CZ  -  NH2 ANGL. DEV. =   7.0 DEGREES          
REMARK 500    ARG A  14   NE  -  CZ  -  NH2 ANGL. DEV. =  -5.1 DEGREES          
REMARK 500    ASP A  48   CB  -  CG  -  OD1 ANGL. DEV. =   5.5 DEGREES          
REMARK 500    ARG A  61   CD  -  NE  -  CZ  ANGL. DEV. =  10.4 DEGREES          
REMARK 500    ARG A  61   NE  -  CZ  -  NH1 ANGL. DEV. =   6.0 DEGREES          
REMARK 500    ARG A  68   CD  -  NE  -  CZ  ANGL. DEV. =  16.7 DEGREES          
REMARK 500    ARG A  73   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.6 DEGREES          
REMARK 500    VAL A  99   CB  -  CA  -  C   ANGL. DEV. = -11.8 DEGREES          
REMARK 500    ASP A 101   CB  -  CG  -  OD1 ANGL. DEV. =   5.6 DEGREES          
REMARK 500    ASP A 101   CB  -  CG  -  OD2 ANGL. DEV. =  -6.2 DEGREES          
REMARK 500    ARG A 112   NE  -  CZ  -  NH1 ANGL. DEV. =  -5.7 DEGREES          
REMARK 500    LYS A 116   O   -  C   -  N   ANGL. DEV. = -10.9 DEGREES          
REMARK 500    ARG A 125   NE  -  CZ  -  NH2 ANGL. DEV. =  -5.3 DEGREES          
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 ASP A  101     GLY A  102                  132.40                    
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  68         0.19    SIDE CHAIN                              
REMARK 500    ARG A 128         0.09    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY                                       
REMARK 500                                                                      
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY                       
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER                 
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;                     
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;                            
REMARK 500 I=INSERTION CODE).                                                   
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        ANGLE                                           
REMARK 500    LEU A  84        -11.84                                           
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  8RLF A    1   129  UNP    P00698   LYSC_CHICK      19    147             
SEQRES   1 A  129  LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS          
SEQRES   2 A  129  ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY          
SEQRES   3 A  129  ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN          
SEQRES   4 A  129  THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP          
SEQRES   5 A  129  TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN          
SEQRES   6 A  129  ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE          
SEQRES   7 A  129  PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER          
SEQRES   8 A  129  VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY          
SEQRES   9 A  129  MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY          
SEQRES  10 A  129  THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU              
HET    NO3  A 201       4                                                       
HET    NO3  A 202       4                                                       
HET    NO3  A 203       4                                                       
HET    NO3  A 204       4                                                       
HET    NO3  A 205       4                                                       
HET    NO3  A 206       4                                                       
HET    NO3  A 207       4                                                       
HET    NO3  A 208       4                                                       
HET    NO3  A 209       4                                                       
HET    ACT  A 210       7                                                       
HETNAM     NO3 NITRATE ION                                                      
HETNAM     ACT ACETATE ION                                                      
FORMUL   2  NO3    9(N O3 1-)                                                   
FORMUL  11  ACT    C2 H3 O2 1-                                                  
FORMUL  12  HOH   *108(H2 O)                                                    
HELIX    1 AA1 GLY A    4  HIS A   15  1                                  12    
HELIX    2 AA2 ASN A   19  TYR A   23  5                                   5    
HELIX    3 AA3 SER A   24  ASN A   37  1                                  14    
HELIX    4 AA4 PRO A   79  SER A   85  5                                   7    
HELIX    5 AA5 ILE A   88  ASP A  101  1                                  14    
HELIX    6 AA6 GLY A  104  ALA A  107  5                                   4    
HELIX    7 AA7 TRP A  108  CYS A  115  1                                   8    
HELIX    8 AA8 ASP A  119  ILE A  124  5                                   6    
SHEET    1 AA1 3 THR A  43  ARG A  45  0                                        
SHEET    2 AA1 3 THR A  51  TYR A  53 -1  O  ASP A  52   N  ASN A  44           
SHEET    3 AA1 3 ILE A  58  ASN A  59 -1  O  ILE A  58   N  TYR A  53           
SSBOND   1 CYS A    6    CYS A  127                          1555   1555  2.03  
SSBOND   2 CYS A   30    CYS A  115                          1555   1555  2.03  
SSBOND   3 CYS A   64    CYS A   80                          1555   1555  2.03  
SSBOND   4 CYS A   76    CYS A   94                          1555   1555  2.03  
CRYST1   27.250   31.930   34.270  88.52  71.37  68.16 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      0.036697 -0.014708 -0.014005        0.00000                         
SCALE2      0.000000  0.033740  0.003588        0.00000                         
SCALE3      0.000000  0.000000  0.030967        0.00000