HEADER    RETINOL-BINDING PROTEIN                 18-JUL-16   5LJK              
TITLE     CRYSTAL STRUCTURE OF HUMAN APO CRBP1                                  
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: RETINOL-BINDING PROTEIN 1;                                 
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: CELLULAR RETINOL-BINDING PROTEIN,CRBP,CELLULAR RETINOL-     
COMPND   5 BINDING PROTEIN I,CRBP-I;                                            
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: RBP1, CRBP1;                                                   
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);                       
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008                                      
KEYWDS    RETINOL, VITAMIN A, RETINOL-BINDING PROTEIN, RBP                      
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    G.ZANOTTI,F.VALLESE,R.BERNI,I.MENOZZI                                 
REVDAT   3   10-JAN-24 5LJK    1       LINK                                     
REVDAT   2   29-MAR-17 5LJK    1       JRNL                                     
REVDAT   1   18-JAN-17 5LJK    0                                                
JRNL        AUTH   I.MENOZZI,F.VALLESE,E.POLVERINI,C.FOLLI,R.BERNI,G.ZANOTTI    
JRNL        TITL   STRUCTURAL AND MOLECULAR DETERMINANTS AFFECTING THE          
JRNL        TITL 2 INTERACTION OF RETINOL WITH HUMAN CRBP1.                     
JRNL        REF    J. STRUCT. BIOL.              V. 197   330 2017              
JRNL        REFN                   ESSN 1095-8657                               
JRNL        PMID   28057518                                                     
JRNL        DOI    10.1016/J.JSB.2016.12.012                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.70 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX (1.10.1_2155: ???)                            
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : NULL                                          
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 40.53                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.380                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.6                           
REMARK   3   NUMBER OF REFLECTIONS             : 14198                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.206                           
REMARK   3   R VALUE            (WORKING SET) : 0.204                           
REMARK   3   FREE R VALUE                     : 0.251                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.780                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 678                             
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 40.5369 -  2.9069    1.00     2845   141  0.1636 0.1986        
REMARK   3     2  2.9069 -  2.3074    1.00     2696   150  0.2278 0.2964        
REMARK   3     3  2.3074 -  2.0157    1.00     2686   132  0.2421 0.2919        
REMARK   3     4  2.0157 -  1.8314    1.00     2672   131  0.2338 0.2928        
REMARK   3     5  1.8314 -  1.7001    0.99     2621   124  0.2910 0.3314        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.240            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.330           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.016           1142                                  
REMARK   3   ANGLE     :  1.223           1539                                  
REMARK   3   CHIRALITY :  0.058            165                                  
REMARK   3   PLANARITY :  0.006            198                                  
REMARK   3   DIHEDRAL  : 12.774            695                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 5LJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-16.                  
REMARK 100 THE DEPOSITION ID IS D_1200000838.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 22-JUN-16                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 5                                  
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : ESRF                               
REMARK 200  BEAMLINE                       : ID30B                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.973186                           
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          : SCALA                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 14255                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.700                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 47.890                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.8                               
REMARK 200  DATA REDUNDANCY                : 9.400                              
REMARK 200  R MERGE                    (I) : 0.13200                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 7.4000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.76                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 98.5                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 6.70                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.89000                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: MOLREP                                                
REMARK 200 STARTING MODEL: 5LJB                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 40.00                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CHLORIDE, 0.1 M SODIUM    
REMARK 280  ACETATE, 0.2 MM ZINC CHLORIDE, PH 5,0, 20% PEG 6000, VAPOR          
REMARK 280  DIFFUSION, TEMPERATURE 279K                                         
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
REMARK 290       4555   X+1/2,-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       17.03050            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       38.03200            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       23.94400            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       38.03200            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       17.03050            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       23.94400            
REMARK 290   SMTRY3   4  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: 90 ANGSTROM**2                            
REMARK 350 SURFACE AREA OF THE COMPLEX: 7470 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     MET A     0                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
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   OE2  GLU A    18    NA     NA A   201              1.57            
REMARK 500   OD2  ASP A   113     O    HOH A   301              2.17            
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    LEU A  74       31.88    -92.35                                   
REMARK 500    ILE A  77      -85.75    -91.79                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              NA A 201  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 GLU A  18   OE1                                                    
REMARK 620 2 ASP A  63   OD1  27.4                                              
REMARK 620 3 HOH A 322   O    75.8  66.3                                        
REMARK 620 4 HOH A 351   O    82.5  68.6 119.2                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 201                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 5LJB   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5LJC   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5LJD   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5LJE   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5LJG   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 5LJK   RELATED DB: PDB                                   
DBREF  5LJK A    0   134  UNP    P09455   RET1_HUMAN       1    135             
SEQRES   1 A  135  MET PRO VAL ASP PHE THR GLY TYR TRP LYS MET LEU VAL          
SEQRES   2 A  135  ASN GLU ASN PHE GLU GLU TYR LEU ARG ALA LEU ASP VAL          
SEQRES   3 A  135  ASN VAL ALA LEU ARG LYS ILE ALA ASN LEU LEU LYS PRO          
SEQRES   4 A  135  ASP LYS GLU ILE VAL GLN ASP GLY ASP HIS MET ILE ILE          
SEQRES   5 A  135  ARG THR LEU SER THR PHE ARG ASN TYR ILE MET ASP PHE          
SEQRES   6 A  135  GLN VAL GLY LYS GLU PHE GLU GLU ASP LEU THR GLY ILE          
SEQRES   7 A  135  ASP ASP ARG LYS CYS MET THR THR VAL SER TRP ASP GLY          
SEQRES   8 A  135  ASP LYS LEU GLN CYS VAL GLN LYS GLY GLU LYS GLU GLY          
SEQRES   9 A  135  ARG GLY TRP THR GLN TRP ILE GLU GLY ASP GLU LEU HIS          
SEQRES  10 A  135  LEU GLU MET ARG VAL GLU GLY VAL VAL CYS LYS GLN VAL          
SEQRES  11 A  135  PHE LYS LYS VAL GLN                                          
HET     NA  A 201       1                                                       
HETNAM      NA SODIUM ION                                                       
FORMUL   2   NA    NA 1+                                                        
FORMUL   3  HOH   *124(H2 O)                                                    
HELIX    1 AA1 ASN A   15  LEU A   23  1                                   9    
HELIX    2 AA2 ASN A   26  LEU A   36  1                                  11    
SHEET    1 AA110 TYR A  60  GLN A  65  0                                        
SHEET    2 AA110 HIS A  48  LEU A  54 -1  N  THR A  53   O  TYR A  60           
SHEET    3 AA110 ASP A  39  ASP A  45 -1  N  GLU A  41   O  ARG A  52           
SHEET    4 AA110 GLY A   6  GLU A  14 -1  N  TRP A   8   O  LYS A  40           
SHEET    5 AA110 VAL A 124  LYS A 131 -1  O  VAL A 129   N  LEU A  11           
SHEET    6 AA110 GLU A 114  VAL A 121 -1  N  LEU A 117   O  GLN A 128           
SHEET    7 AA110 GLY A 105  GLU A 111 -1  N  TRP A 109   O  HIS A 116           
SHEET    8 AA110 LYS A  92  LYS A  98 -1  N  LEU A  93   O  GLN A 108           
SHEET    9 AA110 LYS A  81  ASP A  89 -1  N  ASP A  89   O  LYS A  92           
SHEET   10 AA110 PHE A  70  ASP A  73 -1  N  PHE A  70   O  THR A  84           
LINK         OE1 GLU A  18                NA    NA A 201     1555   1555  3.12  
LINK         OD1 ASP A  63                NA    NA A 201     1555   1655  3.04  
LINK        NA    NA A 201                 O   HOH A 322     1555   1555  1.98  
LINK        NA    NA A 201                 O   HOH A 351     1555   1555  1.99  
SITE     1 AC1  4 GLU A  18  ASP A  63  HOH A 322  HOH A 351                    
CRYST1   34.061   47.888   76.064  90.00  90.00  90.00 P 21 21 21    4          
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      0.029359  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.020882  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.013147        0.00000