10 20 30 40 50 60 70 80 2IDV - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSLATION REGULATOR 15-SEP-06 2IDV
TITLE CRYSTAL STRUCTURE OF WHEAT C113S MUTANT EIF4E BOUND TO 7- TITLE 2 METHYL-GDP
COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 39-215; COMPND 5 SYNONYM: EIF4E-1, EIF-4E-1, MRNA CAP-BINDING PROTEIN, EIF- COMPND 6 4F 25 KDA SUBUNIT, EIF-4F P26 SUBUNIT; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRITICUM AESTIVUM; SOURCE 3 ORGANISM_COMMON: BREAD WHEAT; SOURCE 4 ORGANISM_TAXID: 4565; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS EUKARYOTIC INITIATION FACTOR 4E, EIF4E, CAP, METHYL-7-GDP, KEYWDS 2 TRANSLATION REGULATOR
EXPDTA X-RAY DIFFRACTION
AUTHOR A.F.MONZINGO,A.DUTT-CHAUDHURI,J.SADOW,S.DHALIWAL, AUTHOR 2 D.W.HOFFMAN,J.D.ROBERTUS,K.S.BROWNING
REVDAT 2 24-FEB-09 2IDV 1 VERSN REVDAT 1 12-JUN-07 2IDV 0
JRNL AUTH A.F.MONZINGO,S.DHALIWAL,A.DUTT-CHAUDHURI,A.LYON, JRNL AUTH 2 J.H.SADOW,D.W.HOFFMAN,J.D.ROBERTUS,K.S.BROWNING JRNL TITL THE STRUCTURE OF EUKARYOTIC TRANSLATION INITIATION JRNL TITL 2 FACTOR-4E FROM WHEAT REVEALS A NOVEL DISULFIDE JRNL TITL 3 BOND. JRNL REF PLANT PHYSIOL. V. 143 1504 2007 JRNL REFN ISSN 0032-0889 JRNL PMID 17322339 JRNL DOI 10.1104/PP.106.093146
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 6372 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) : 0.200 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 301 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 717 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 31 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 : 1428 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 101 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.59 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.238 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.969 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.796 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.502 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 26.84 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : M7G.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : M7G.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2IDV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-06. REMARK 100 THE RCSB ID CODE IS RCSB039460.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : BLUE MAX-FLUX CONFOCAL REMARK 200 OPTICAL SYSTEM REMARK 200 OPTICS : BLUE MAX-FLUX CONFOCAL REMARK 200 OPTICAL SYSTEM REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6939 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.14700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 12.400 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: PDB ENTRY 1EJ1 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG4000, 0.1 M HEPES, 20 MM REMARK 280 PHENOL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.11350 REMARK 290 SMTRY3 2 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 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 LYS A 160 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 SER A 205 OG
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 ASP A 51 110.67 -162.96 REMARK 500 ASN A 102 -123.86 47.10 REMARK 500 GLN A 159 -78.34 -40.93 REMARK 500 ARG A 204 102.67 -52.84 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 M7G A 1000
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IDR RELATED DB: PDB REMARK 900 WILD-TYPE EIF4E
DBREF 2IDV A 39 215 UNP P29557 IF4E1_WHEAT 39 215
SEQADV 2IDV SER A 113 UNP P29557 CYS 113 ENGINEERED
SEQRES 1 A 177 ALA HIS PRO LEU GLU ASN ALA TRP THR PHE TRP PHE ASP SEQRES 2 A 177 ASN PRO GLN GLY LYS SER ARG GLN VAL ALA TRP GLY SER SEQRES 3 A 177 THR ILE HIS PRO ILE HIS THR PHE SER THR VAL GLU ASP SEQRES 4 A 177 PHE TRP GLY LEU TYR ASN ASN ILE HIS ASN PRO SER LYS SEQRES 5 A 177 LEU ASN VAL GLY ALA ASP PHE HIS CYS PHE LYS ASN LYS SEQRES 6 A 177 ILE GLU PRO LYS TRP GLU ASP PRO ILE SER ALA ASN GLY SEQRES 7 A 177 GLY LYS TRP THR ILE SER CYS GLY ARG GLY LYS SER ASP SEQRES 8 A 177 THR PHE TRP LEU HIS THR LEU LEU ALA MET ILE GLY GLU SEQRES 9 A 177 GLN PHE ASP PHE GLY ASP GLU ILE CYS GLY ALA VAL VAL SEQRES 10 A 177 SER VAL ARG GLN LYS GLN GLU ARG VAL ALA ILE TRP THR SEQRES 11 A 177 LYS ASN ALA ALA ASN GLU ALA ALA GLN ILE SER ILE GLY SEQRES 12 A 177 LYS GLN TRP LYS GLU PHE LEU ASP TYR LYS ASP SER ILE SEQRES 13 A 177 GLY PHE ILE VAL HIS GLU ASP ALA LYS ARG SER ASP LYS SEQRES 14 A 177 GLY PRO LYS ASN ARG TYR THR VAL
HET M7G A1000 29
HETNAM M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
FORMUL 2 M7G C11 H19 N5 O11 P2 FORMUL 3 HOH *101(H2 O)
HELIX 1 1 VAL A 75 ASN A 84 1 10 HELIX 2 2 ASN A 87 LEU A 91 5 5 HELIX 3 3 ASP A 110 ALA A 114 5 5 HELIX 4 4 SER A 128 GLY A 141 1 14 HELIX 5 5 PHE A 146 ASP A 148 5 3 HELIX 6 6 ASN A 173 ASP A 189 1 17 HELIX 7 7 HIS A 199 LYS A 203 1 5
SHEET 1 A 8 HIS A 67 THR A 74 0 SHEET 2 A 8 PRO A 41 ASP A 51 -1 N PHE A 48 O ILE A 69 SHEET 3 A 8 ASP A 96 LYS A 101 -1 O HIS A 98 N TRP A 49 SHEET 4 A 8 ILE A 150 VAL A 157 -1 O CYS A 151 N LYS A 101 SHEET 5 A 8 GLU A 162 THR A 168 -1 O ARG A 163 N SER A 156 SHEET 6 A 8 GLY A 117 CYS A 123 -1 N CYS A 123 O GLU A 162 SHEET 7 A 8 ILE A 194 VAL A 198 -1 O ILE A 197 N LYS A 118 SHEET 8 A 8 TYR A 213 VAL A 215 -1 O VAL A 215 N ILE A 194
SITE 1 AC1 12 ARG A 58 TRP A 62 LYS A 107 TRP A 108 SITE 2 AC1 12 GLU A 109 ARG A 158 ARG A 163 HOH A1012 SITE 3 AC1 12 HOH A1066 HOH A1076 HOH A1092 HOH A1093
CRYST1 36.651 58.227 39.063 90.00 115.85 90.00 P 1 21 1 2
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 0.027284 0.000000 0.013219 0.00000
SCALE2 0.000000 0.017174 0.000000 0.00000
SCALE3 0.000000 0.000000 0.028446 0.00000