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Database: PDB
Entry: 4GIF
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Original site: 4GIF 
HEADER    TRANSPORT PROTEIN                       08-AUG-12   4GIF              
TITLE     C-TERMINAL COILED-COIL DOMAIN OF TRANSIENT RECEPTOR POTENTIAL CHANNEL 
TITLE    2 TRPP3 (PKD2L1, POLYCYSTIN-L)                                         
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: POLYCYSTIC KIDNEY DISEASE 2-LIKE 1 PROTEIN;                
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: UNP RESIDUES 699-743;                                      
COMPND   5 SYNONYM: POLYCYSTIN-2 HOMOLOG, POLYCYSTIN-2L1, POLYCYSTIN-L,         
COMPND   6 POLYCYSTIN-L1;                                                       
COMPND   7 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: PKD2L1, PKD2L, PKDL;                                           
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    COILED-COIL, TRIMER, TRP CHANNEL, TRANSIENT RECEPTOR POTENTIAL        
KEYWDS   2 CHANNEL, POLYCYSTIC KIDNEY DISEASE (PKD), MEMBRANE, TRANSPORT        
KEYWDS   3 PROTEIN                                                              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    Y.YU,M.H.ULBRICH,M.-H.LI,S.DOBBINS,W.K.ZHANG,L.TONG,E.Y.ISACOFF,      
AUTHOR   2 J.YANG                                                               
REVDAT   2   26-DEC-12 4GIF    1       JRNL                                     
REVDAT   1   05-DEC-12 4GIF    0                                                
JRNL        AUTH   Y.YU,M.H.ULBRICH,M.H.LI,S.DOBBINS,W.K.ZHANG,L.TONG,          
JRNL        AUTH 2 E.Y.ISACOFF,J.YANG                                           
JRNL        TITL   MOLECULAR MECHANISM OF THE ASSEMBLY OF AN ACID-SENSING       
JRNL        TITL 2 RECEPTOR ION CHANNEL COMPLEX.                                
JRNL        REF    NAT COMMUN                    V.   3  1252 2012              
JRNL        REFN                   ESSN 2041-1723                               
JRNL        PMID   23212381                                                     
JRNL        DOI    10.1038/NCOMMS2257                                           
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.80 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,              
REMARK   3               : READ,RICE,SIMONSON,WARREN                            
REMARK   3                                                                      
REMARK   3  REFINEMENT TARGET : ENGH & HUBER                                    
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL                           
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL                           
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 97.4                           
REMARK   3   NUMBER OF REFLECTIONS             : 1896                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.235                           
REMARK   3   FREE R VALUE                     : 0.286                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL                            
REMARK   3   FREE R VALUE TEST SET COUNT      : 177                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL                         
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.80                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.90                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL                         
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2670                       
REMARK   3   BIN FREE R VALUE                    : 0.3070                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 14                           
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL                         
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 357                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 0                                       
REMARK   3   SOLVENT ATOMS            : 44                                      
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  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL                            
REMARK   3   ESD FROM SIGMAA              (A) : NULL                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.013                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.60                            
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL                            
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL                            
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : NULL                                      
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : NULL                                                 
REMARK   3   KSOL        : NULL                                                 
REMARK   3   BSOL        : NULL                                                 
REMARK   3                                                                      
REMARK   3  NCS MODEL : NULL                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 4GIF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-12.                  
REMARK 100 THE RCSB ID CODE IS RCSB074222.                                      
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 05-FEB-05                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : NSLS                               
REMARK 200  BEAMLINE                       : X4C                                
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9792                             
REMARK 200  MONOCHROMATOR                  : SI 111 CHANNEL                     
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : MAR CCD 165 MM                     
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 1928                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.800                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.1                               
REMARK 200  DATA REDUNDANCY                : 9.000                              
REMARK 200  R MERGE                    (I) : 0.05500                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 36.7000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.90                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY IN SHELL       : 9.20                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.10300                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 25.200                             
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 64.80                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 18-20% PEG 8000, 100 MM HEPES, PH 7.5,   
REMARK 280  3.9 MM HEGA-9, EVAPORATION, TEMPERATURE 293.0K                      
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1                          
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -Y,X-Y,Z                                                
REMARK 290       3555   -X+Y,-X,Z                                               
REMARK 290       4555   Y,X,-Z                                                  
REMARK 290       5555   X-Y,-Y,-Z                                               
REMARK 290       6555   -X,-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   SMTRY1   2 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   4 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   4  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   5  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   6 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   6 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   6  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: TRIMERIC                          
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC                   
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 TOTAL BURIED SURFACE AREA: 3830 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 10040 ANGSTROM**2                       
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 350   BIOMT1   2 -0.500000 -0.866025  0.000000       44.52700            
REMARK 350   BIOMT2   2  0.866025 -0.500000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   3 -0.500000  0.866025  0.000000       22.26350            
REMARK 350   BIOMT2   3 -0.866025 -0.500000  0.000000       38.56151            
REMARK 350   BIOMT3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 525                                                                      
REMARK 525 SOLVENT                                                              
REMARK 525                                                                      
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT                    
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST                  
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT                 
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE                       
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;                             
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE                  
REMARK 525 NUMBER; I=INSERTION CODE):                                           
REMARK 525                                                                      
REMARK 525  M RES CSSEQI                                                        
REMARK 525    HOH A 823        DISTANCE =  6.34 ANGSTROMS                       
REMARK 525    HOH A 832        DISTANCE =  5.40 ANGSTROMS                       
REMARK 525    HOH A 833        DISTANCE =  5.71 ANGSTROMS                       
REMARK 525    HOH A 836        DISTANCE =  6.10 ANGSTROMS                       
REMARK 525    HOH A 837        DISTANCE =  7.02 ANGSTROMS                       
REMARK 525    HOH A 839        DISTANCE =  6.35 ANGSTROMS                       
REMARK 525    HOH A 844        DISTANCE =  5.91 ANGSTROMS                       
REMARK 999                                                                      
REMARK 999 SEQUENCE                                                             
REMARK 999 THE CRYSTALLIZED SEQUENCE IS:                                        
REMARK 999 MGSSHHHHHHSQDPKEELAGQKDELQLSDLLKQGYNKTLLRLRLRKERVSDVQKVLQGGEQEIQFEDF 
REMARK 999  TNTLRELGHAEHEITELTATFTKFDRDGNRILDEKEQEKMRQDLEEERVALNTEIEKLGRSIVSSPQ 
REMARK 999  GKSGPEAARA(GGWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKLKMLERKGW)           
REMARK 999  LAPSPGVKEQAIWKHPQPAPAVTPDPWGVQGGQESEVPYKREEEALEERRLSRGEIPTLQRS OF   
REMARK 999  WHICH THE SEGMENT LISTED IN SEQRES RECORD WAS OBSERVED IN THE       
REMARK 999  ELECTRON DENSITY. THE AUTHORS BELIEVE THAT THE PROTEIN WAS DEGRADED 
REMARK 999  DURING THE PROCESS OF CRYSTALLIZATION AND ONLY THE COILED COIL      
REMARK 999  DOMAIN WAS CRYSTALLIZATION. TO TEST THIS POSSIBILITY, THE AUTHORS   
REMARK 999  COLLECTED SOME CRYSTALS AND RAN IT ON SDS-PAGE. ONLY A DEGRADED     
REMARK 999  BAND WITH A MOLECULAR WEIGHT MATCH THE COILED COIL DOMAIN WAS SHOWN 
REMARK 999  ON THE GEL. HOWEVER THE AUTHORS DO NOT KNOW HOW MANY AMINO ACIDS    
REMARK 999  ARE MISSING FROM THE N- AND C-TERMINUS DUE TO DISORDER.             
DBREF  4GIF A  699   743  UNP    Q9P0L9   PK2L1_HUMAN    699    743             
SEQRES   1 A   45  GLY GLY TRP VAL SER GLY GLU GLU PHE TYR MET LEU THR          
SEQRES   2 A   45  ARG ARG VAL LEU GLN LEU GLU THR VAL LEU GLU GLY VAL          
SEQRES   3 A   45  VAL SER GLN ILE ASP ALA VAL GLY SER LYS LEU LYS MET          
SEQRES   4 A   45  LEU GLU ARG LYS GLY TRP                                      
FORMUL   2  HOH   *44(H2 O)                                                     
HELIX    1   1 SER A  703  SER A  733  1                                  31    
HELIX    2   2 SER A  733  GLY A  742  1                                  10    
CRYST1   44.527   44.527   62.306  90.00  90.00 120.00 P 3 2 1       6          
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      0.022458  0.012966  0.000000        0.00000                         
SCALE2      0.000000  0.025933  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.016050        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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