HEADER OXIDOREDUCTASE 26-JAN-10 3ADO TITLE CRYSTAL STRUCTURE OF THE RABBIT L-GULONATE 3-DEHYDROGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LAMBDA-CRYSTALLIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-GULONATE 3-DEHYDROGENASE, GUL3DH; COMPND 5 EC: 1.1.1.45; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 GENE: CRYL1, GUL3DH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCR T7/CT-TOPO KEYWDS L-GULONATE 3-DEHYDROGENASE, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, ACETYLATION, CYTOPLASM, EYE KEYWDS 3 LENS PROTEIN, NAD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ASADA,A.HARA,N.KUNISHIMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 01-NOV-23 3ADO 1 REMARK REVDAT 2 26-MAY-10 3ADO 1 SPRSDE REVDAT 1 09-FEB-10 3ADO 0 SPRSDE 26-MAY-10 3ADO 2DPO JRNL AUTH Y.ASADA,A.HARA,N.KUNISHIMA JRNL TITL CRYSTAL STRUCTURE OF THE RABBIT L-GULONATE 3-DEHYDROGENASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.96 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) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34455 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RAMDOM REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1676 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 211 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2403 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 419 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.97000 REMARK 3 B22 (A**2) : -1.44000 REMARK 3 B33 (A**2) : -2.53000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 3ADO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000029122. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : BENDING MAGNET REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34467 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.53700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3HDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE, SODIUM ACETATE REMARK 280 TRIHYDRATE, POLYETHYLENE GLYCOL 4000, GLYCEROL ANHYDROUS, PH 4.6, REMARK 280 MICROBATCH, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.90450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.53950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.90450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.53950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 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 -1.000000 0.000000 0.000000 57.34545 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.02873 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 737 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 PRO A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 6 REMARK 465 GLN A 317 REMARK 465 PRO A 318 REMARK 465 GLN A 319 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 CYS A 125 -39.06 -144.04 REMARK 500 HIS A 137 30.18 -98.68 REMARK 500 PHE A 193 -128.81 49.59 REMARK 500 SER A 273 -164.44 -163.82 REMARK 500 ALA A 290 41.41 -77.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ADP RELATED DB: PDB REMARK 900 RELATED ID: MY_001000051.1 RELATED DB: TARGETDB DBREF 3ADO A 1 319 UNP P14755 CRYL1_RABIT 1 319 SEQRES 1 A 319 MET ALA SER PRO ALA ALA GLY ASP VAL LEU ILE VAL GLY SEQRES 2 A 319 SER GLY LEU VAL GLY ARG SER TRP ALA MET LEU PHE ALA SEQRES 3 A 319 SER GLY GLY PHE ARG VAL LYS LEU TYR ASP ILE GLU PRO SEQRES 4 A 319 ARG GLN ILE THR GLY ALA LEU GLU ASN ILE ARG LYS GLU SEQRES 5 A 319 MET LYS SER LEU GLN GLN SER GLY SER LEU LYS GLY SER SEQRES 6 A 319 LEU SER ALA GLU GLU GLN LEU SER LEU ILE SER SER CYS SEQRES 7 A 319 THR ASN LEU ALA GLU ALA VAL GLU GLY VAL VAL HIS ILE SEQRES 8 A 319 GLN GLU CYS VAL PRO GLU ASN LEU ASP LEU LYS ARG LYS SEQRES 9 A 319 ILE PHE ALA GLN LEU ASP SER ILE VAL ASP ASP ARG VAL SEQRES 10 A 319 VAL LEU SER SER SER SER SER CYS LEU LEU PRO SER LYS SEQRES 11 A 319 LEU PHE THR GLY LEU ALA HIS VAL LYS GLN CYS ILE VAL SEQRES 12 A 319 ALA HIS PRO VAL ASN PRO PRO TYR TYR ILE PRO LEU VAL SEQRES 13 A 319 GLU LEU VAL PRO HIS PRO GLU THR SER PRO ALA THR VAL SEQRES 14 A 319 ASP ARG THR HIS ALA LEU MET ARG LYS ILE GLY GLN SER SEQRES 15 A 319 PRO VAL ARG VAL LEU LYS GLU ILE ASP GLY PHE VAL LEU SEQRES 16 A 319 ASN ARG LEU GLN TYR ALA ILE ILE SER GLU ALA TRP ARG SEQRES 17 A 319 LEU VAL GLU GLU GLY ILE VAL SER PRO SER ASP LEU ASP SEQRES 18 A 319 LEU VAL MET SER ASP GLY LEU GLY MET ARG TYR ALA PHE SEQRES 19 A 319 ILE GLY PRO LEU GLU THR MET HIS LEU ASN ALA GLU GLY SEQRES 20 A 319 MET LEU SER TYR CYS ASP ARG TYR SER GLU GLY MET LYS SEQRES 21 A 319 ARG VAL LEU LYS SER PHE GLY SER ILE PRO GLU PHE SER SEQRES 22 A 319 GLY ALA THR VAL GLU LYS VAL ASN GLN ALA MET CYS LYS SEQRES 23 A 319 LYS VAL PRO ALA ASP PRO GLU HIS LEU ALA ALA ARG ARG SEQRES 24 A 319 GLU TRP ARG ASP GLU CYS LEU LYS ARG LEU ALA LYS LEU SEQRES 25 A 319 LYS ARG GLN MET GLN PRO GLN FORMUL 2 HOH *419(H2 O) HELIX 1 1 GLY A 15 GLY A 28 1 14 HELIX 2 2 GLU A 38 SER A 59 1 22 HELIX 3 3 SER A 67 LEU A 74 1 8 HELIX 4 4 ASN A 80 VAL A 85 1 6 HELIX 5 5 ASN A 98 SER A 111 1 14 HELIX 6 6 LEU A 127 THR A 133 1 7 HELIX 7 7 HIS A 137 LYS A 139 5 3 HELIX 8 8 SER A 165 ILE A 179 1 15 HELIX 9 9 VAL A 194 GLU A 212 1 19 HELIX 10 10 SER A 216 ASP A 226 1 11 HELIX 11 11 GLY A 227 ALA A 233 1 7 HELIX 12 12 GLY A 236 ASN A 244 1 9 HELIX 13 13 GLY A 247 SER A 265 1 19 HELIX 14 14 SER A 273 VAL A 288 1 16 HELIX 15 15 ASP A 291 MET A 316 1 26 SHEET 1 A 8 ILE A 75 CYS A 78 0 SHEET 2 A 8 VAL A 32 TYR A 35 1 N LEU A 34 O SER A 76 SHEET 3 A 8 ASP A 8 VAL A 12 1 N ILE A 11 O LYS A 33 SHEET 4 A 8 VAL A 88 GLU A 93 1 O GLN A 92 N LEU A 10 SHEET 5 A 8 VAL A 118 SER A 121 1 O SER A 120 N GLU A 93 SHEET 6 A 8 CYS A 141 PRO A 146 1 O ALA A 144 N SER A 121 SHEET 7 A 8 LEU A 155 PRO A 160 -1 O GLU A 157 N HIS A 145 SHEET 8 A 8 SER A 182 ARG A 185 1 O VAL A 184 N LEU A 158 CISPEP 1 ASN A 148 PRO A 149 0 -0.31 CRYST1 71.809 69.079 65.642 90.00 102.73 90.00 C 1 2 1 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 0.013926 0.000000 0.003146 0.00000 SCALE2 0.000000 0.014476 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015618 0.00000