HEADER STRUCTURAL PROTEIN 27-APR-05 1ZIE TITLE HYDROGENATED GAMMAE CRYSTALLIN IN D2O SOLVENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA CRYSTALLIN E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAMMA CRYSTALLIN 3-1, GAMMA-2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS 4 GREEK KEY MOTIFS, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.B.ARTERO,M.HARTLEIN,S.MCSWEENEY,P.TIMMINS REVDAT 4 25-OCT-23 1ZIE 1 REMARK REVDAT 3 13-JUL-11 1ZIE 1 VERSN REVDAT 2 24-FEB-09 1ZIE 1 VERSN REVDAT 1 08-NOV-05 1ZIE 0 JRNL AUTH J.B.ARTERO,M.HARTLEIN,S.MCSWEENEY,P.TIMMINS JRNL TITL A COMPARISON OF REFINED X-RAY STRUCTURES OF HYDROGENATED AND JRNL TITL 2 PERDEUTERATED RAT GAMMAE-CRYSTALLIN IN H2O AND D2O. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 1541 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 16239733 JRNL DOI 10.1107/S0907444905028532 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.174 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.172 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1324 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 30005 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 : 1477 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 202 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) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 1.766 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 : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000032757. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : A DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30005 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 50.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 1A5D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MAGNESIUM ACETATE, D2O, PH REMARK 280 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 18.81500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.93000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.71000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.93000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.81500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.71000 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 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 TYR A 1173 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 TYR A1006 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A1009 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 TYR A1055 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A1094 CD - NE - CZ ANGL. DEV. = 12.0 DEGREES REMARK 500 ARG A1094 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A1094 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A1114 O - C - N ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG A1141 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A1151 NE - CZ - NH1 ANGL. DEV. = 3.3 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 SER A1072 -177.73 -171.37 REMARK 500 PHE A1115 -163.54 -107.11 REMARK 500 HIS A1116 79.61 44.86 REMARK 500 SER A1118 -15.81 140.02 REMARK 500 ASP A1119 161.80 158.17 REMARK 500 ASP A1171 159.56 -35.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 2378 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 2380 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A5D RELATED DB: PDB REMARK 900 NATIVE RAT GAMMAE CRYSTALLIN REMARK 900 RELATED ID: 1ZGT RELATED DB: PDB REMARK 900 RECOMBINANT HYDROGENATED GAMMAE CRYSTALLIN IN H2O REMARK 900 RELATED ID: 1ZIQ RELATED DB: PDB REMARK 900 DEUTERATED GAMMAE CRYSTALLIN IN D2O REMARK 900 RELATED ID: 1ZIR RELATED DB: PDB REMARK 900 DEUTERATED GAMMAE CRYSTALLIN IN H2O DBREF 1ZIE A 1001 1173 UNP P02528 CRGE_RAT 1 173 SEQRES 1 A 173 GLY LYS ILE THR PHE TYR GLU ASP ARG GLY PHE GLN GLY SEQRES 2 A 173 ARG HIS TYR GLU CYS SER THR ASP HIS SER ASN LEU GLN SEQRES 3 A 173 PRO TYR PHE SER ARG CYS ASN SER VAL ARG VAL ASP SER SEQRES 4 A 173 GLY CYS TRP MET LEU TYR GLU GLN PRO ASN PHE THR GLY SEQRES 5 A 173 CYS GLN TYR PHE LEU ARG ARG GLY ASP TYR PRO ASP TYR SEQRES 6 A 173 GLN GLN TRP MET GLY PHE SER ASP SER VAL ARG SER CYS SEQRES 7 A 173 ARG LEU ILE PRO HIS SER SER SER HIS ARG ILE ARG ILE SEQRES 8 A 173 TYR GLU ARG GLU ASP TYR ARG GLY GLN MET VAL GLU ILE SEQRES 9 A 173 THR ASP ASP CYS PRO HIS LEU GLN ASP ARG PHE HIS PHE SEQRES 10 A 173 SER ASP PHE HIS SER PHE HIS VAL MET GLU GLY TYR TRP SEQRES 11 A 173 VAL LEU TYR GLU MET PRO ASN TYR ARG GLY ARG GLN TYR SEQRES 12 A 173 LEU LEU ARG PRO GLY GLU TYR ARG ARG TYR HIS ASP TRP SEQRES 13 A 173 GLY ALA MET ASN ALA ARG VAL GLY SER LEU ARG ARG ILE SEQRES 14 A 173 MET ASP PHE TYR HET ACT A2378 4 HET ACT A2380 4 HETNAM ACT ACETATE ION FORMUL 2 ACT 2(C2 H3 O2 1-) FORMUL 4 DOD *202(D2 O) HELIX 1 1 ARG A 1009 PHE A 1011 5 3 HELIX 2 2 ASP A 1064 MET A 1069 5 6 HELIX 3 3 GLU A 1095 TYR A 1097 5 3 HELIX 4 4 HIS A 1110 PHE A 1115 1 6 HELIX 5 5 ARG A 1152 GLY A 1157 5 6 SHEET 1 A 4 GLN A1012 CYS A1018 0 SHEET 2 A 4 LYS A1002 ASP A1008 -1 N ILE A1003 O CYS A1018 SHEET 3 A 4 SER A1034 SER A1039 -1 O ARG A1036 N THR A1004 SHEET 4 A 4 GLY A1060 TYR A1062 -1 O GLY A1060 N VAL A1037 SHEET 1 B 3 THR A1051 LEU A1057 0 SHEET 2 B 3 CYS A1041 GLN A1047 -1 N LEU A1044 O TYR A1055 SHEET 3 B 3 SER A1077 ILE A1081 -1 O ILE A1081 N CYS A1041 SHEET 1 C 4 ARG A1098 ILE A1104 0 SHEET 2 C 4 ARG A1088 ARG A1094 -1 N ILE A1091 O VAL A1102 SHEET 3 C 4 SER A1122 GLU A1127 -1 O HIS A1124 N ARG A1090 SHEET 4 C 4 GLY A1148 TYR A1150 -1 O GLY A1148 N VAL A1125 SHEET 1 D 3 ARG A1139 LEU A1145 0 SHEET 2 D 3 TRP A1130 MET A1135 -1 N TRP A1130 O LEU A1145 SHEET 3 D 3 SER A1165 ARG A1168 -1 O SER A1165 N TYR A1133 SITE 1 AC1 6 GLY A1001 GLY A1040 LEU A1080 DOD A3013 SITE 2 AC1 6 DOD A3045 DOD A3152 SITE 1 AC2 6 LEU A1144 ARG A1146 TYR A1150 DOD A3020 SITE 2 AC2 6 DOD A3064 DOD A3143 CRYST1 37.630 43.420 101.860 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 0.026575 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023031 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009817 0.00000