PDB Short entry for 1HK0 HEADER EYE LENS PROTEIN 05-MAR-03 1HK0 TITLE HUMAN GAMMAD CRYSTALLIN STRUCTURE AT 1.25 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-CRYSTALLIN D; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: GAMMA-D-CRYSTALLIN,GAMMA-CRYSTALLIN 4; COMPND 5 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: CRYGD, CRYG4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS KEYWDS EYE LENS PROTEIN, CATARACT EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BASAK,C.SLINGSBY REVDAT 4 13-DEC-23 1HK0 1 REMARK REVDAT 3 12-DEC-18 1HK0 1 TITLE COMPND SOURCE JRNL REVDAT 3 2 1 REMARK DBREF REVDAT 2 24-FEB-09 1HK0 1 VERSN REVDAT 1 08-MAY-03 1HK0 0 JRNL AUTH A.K.BASAK,O.BATEMAN,C.SLINGSBY,A.PANDE,N.ASHERIE,O.OGUN, JRNL AUTH 2 G.BENEDEK,J.PANDE JRNL TITL HIGH-RESOLUTION X-RAY CRYSTAL STRUCTURES OF HUMAN GAMMAD JRNL TITL 2 CRYSTALLIN (1.25A) AND THE R58H MUTANT (1.15A) ASSOCIATED JRNL TITL 3 WITH ACULEIFORM CATARACT JRNL REF J.MOL.BIOL. V. 328 1137 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12729747 JRNL DOI 10.1016/S0022-2836(03)00375-9 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.YU,N.NEVSKAYA,E.VERNOSLOVA,S.NIKONOV,S.YU,E.BRAZHNIKOV, REMARK 1 AUTH 2 N.FOMENKOVA,V.LUNIN,A.URZHUMTSEV REMARK 1 TITL CRYSTAL STRUCTURE OF CALF EYE LENS GAMMA-CRYSTALLIN IIIB AT REMARK 1 TITL 2 2.5 A RESOLUTION: ITS RELATION TO FUNCTION REMARK 1 REF EXP.EYE RES. V. 53 295 1991 REMARK 1 REFN ISSN 0014-4835 REMARK 1 PMID 1936165 REMARK 1 DOI 10.1016/0014-4835(91)90233-5 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 35783 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 + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.300 REMARK 3 FREE R VALUE TEST SET COUNT : 3238 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1447 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 282 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.66000 REMARK 3 B22 (A**2) : -1.14000 REMARK 3 B33 (A**2) : 0.48000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.877 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1HK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1290012271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : LAUE DIAMOND C111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39066 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 28.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.04800 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) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.18900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1ELP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM PHOSPHATE, 4 DEGREE CELSIUS, PH REMARK 280 7.00, TEMPERATURE 277K 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 16.61000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.23400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.48550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.23400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.61000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.48550 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU X 17 CG CD OE1 OE2 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 O HOH X 2157 O HOH X 2230 1.91 REMARK 500 O ASP X 61 O HOH X 2128 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 ASP X 64 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP X 64 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP X 172 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES 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 X 29 115.55 -161.63 REMARK 500 REMARK 500 REMARK: NULL 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 X2032 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH X2084 DISTANCE = 6.03 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H4A RELATED DB: PDB REMARK 900 HUMAN GAMMA-D CRYSTALLIN R58H MUTANT STRUCTURE AT 1.15 A RESOLUTION REMARK 900 RELATED ID: 1LD0 RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF HUMAN GAMMA D CRYSTALLIN DBREF 1HK0 X 1 174 UNP P07320 CRGD_HUMAN 2 174 SEQRES 1 X 173 GLY LYS ILE THR LEU TYR GLU ASP ARG GLY PHE GLN GLY SEQRES 2 X 173 ARG HIS TYR GLU CYS SER SER ASP HIS PRO ASN LEU GLN SEQRES 3 X 173 PRO TYR LEU SER ARG CYS ASN SER ALA ARG VAL ASP SER SEQRES 4 X 173 GLY CYS TRP MET LEU TYR GLU GLN PRO ASN TYR SER GLY SEQRES 5 X 173 LEU GLN TYR PHE LEU ARG ARG GLY ASP TYR ALA ASP HIS SEQRES 6 X 173 GLN GLN TRP MET GLY LEU SER ASP SER VAL ARG SER CYS SEQRES 7 X 173 ARG LEU ILE PRO HIS SER GLY SER HIS ARG ILE ARG LEU SEQRES 8 X 173 TYR GLU ARG GLU ASP TYR ARG GLY GLN MET ILE GLU PHE SEQRES 9 X 173 THR GLU ASP CYS SER CYS LEU GLN ASP ARG PHE ARG PHE SEQRES 10 X 173 ASN GLU ILE HIS SER LEU ASN VAL LEU GLU GLY SER TRP SEQRES 11 X 173 VAL LEU TYR GLU LEU SER ASN TYR ARG GLY ARG GLN TYR SEQRES 12 X 173 LEU LEU MET PRO GLY ASP TYR ARG ARG TYR GLN ASP TRP SEQRES 13 X 173 GLY ALA THR ASN ALA ARG VAL GLY SER LEU ARG ARG VAL SEQRES 14 X 173 ILE ASP PHE SER FORMUL 2 HOH *282(H2 O) HELIX 1 1 ASP X 64 MET X 69 5 6 HELIX 2 2 GLU X 96 TYR X 98 5 3 HELIX 3 3 CYS X 111 ARG X 115 5 5 HELIX 4 4 ARG X 153 GLY X 158 5 6 SHEET 1 XA 4 GLN X 12 CYS X 18 0 SHEET 2 XA 4 ILE X 3 ASP X 8 -1 O ILE X 3 N CYS X 18 SHEET 3 XA 4 SER X 34 GLN X 47 -1 O SER X 34 N TYR X 6 SHEET 4 XA 4 SER X 51 TYR X 62 -1 O SER X 51 N GLN X 47 SHEET 1 XB 4 GLN X 12 CYS X 18 0 SHEET 2 XB 4 ILE X 3 ASP X 8 -1 O ILE X 3 N CYS X 18 SHEET 3 XB 4 SER X 34 GLN X 47 -1 O SER X 34 N TYR X 6 SHEET 4 XB 4 SER X 77 ILE X 81 -1 O SER X 77 N TYR X 45 SHEET 1 XC 4 ARG X 99 PHE X 105 0 SHEET 2 XC 4 ARG X 89 ARG X 95 -1 O ILE X 90 N PHE X 105 SHEET 3 XC 4 SER X 123 GLU X 128 -1 O SER X 123 N TYR X 93 SHEET 4 XC 4 GLY X 149 TYR X 151 -1 O GLY X 149 N VAL X 126 SHEET 1 XD 3 ARG X 140 LEU X 146 0 SHEET 2 XD 3 TRP X 131 LEU X 136 -1 O TRP X 131 N LEU X 146 SHEET 3 XD 3 SER X 166 ARG X 169 -1 O SER X 166 N TYR X 134 CRYST1 33.220 52.971 90.468 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 0.030102 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018878 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011054 0.00000