HEADER GENE REGULATION 20-MAY-99 1QDE TITLE CRYSTAL STRUCTURE OF THE ATPASE DOMAIN OF TRANSLATION INITIATION TITLE 2 FACTOR 4A FROM SACCHAROMYCES CEREVISIAE-THE PROTOTYPE OF THE DEAD BOX TITLE 3 PROTEIN FAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATION INITIATION FACTOR 4A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 9-232; COMPND 5 SYNONYM: EIF4A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS TRANSLATION INITIATION, SACCHAROMYCES CEREVISIAE, DEAD BOX PROTEIN KEYWDS 2 FAMILY, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR J.BENZ,H.TRACHSEL,U.BAUMANN REVDAT 4 14-FEB-24 1QDE 1 REMARK REVDAT 3 24-FEB-09 1QDE 1 VERSN REVDAT 2 01-APR-03 1QDE 1 JRNL REVDAT 1 23-MAY-00 1QDE 0 JRNL AUTH J.BENZ,H.TRACHSEL,U.BAUMANN JRNL TITL CRYSTAL STRUCTURE OF THE ATPASE DOMAIN OF TRANSLATION JRNL TITL 2 INITIATION FACTOR 4A FROM SACCHAROMYCES CEREVISIAE--THE JRNL TITL 3 PROTOTYPE OF THE DEAD BOX PROTEIN FAMILY. JRNL REF STRUCTURE FOLD.DES. V. 7 671 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10404596 JRNL DOI 10.1016/S0969-2126(99)80088-4 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 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) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 14918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1483 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1588 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.40 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 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 1QDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000009105. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.8 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14988 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.070 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.31500 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: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MGCL2, (NH4)2SO4, MES, PH REMARK 280 4.8, VAPOR DIFFUSION, SITTING 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 19.44000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.02500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.64000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.02500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.44000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.64000 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 GLU A 8 REMARK 465 GLU A 9 REMARK 465 SER A 10 REMARK 465 GLN A 11 REMARK 465 GLY A 126 REMARK 465 THR A 127 REMARK 465 SER A 128 REMARK 465 PHE A 129 REMARK 465 VAL A 130 REMARK 465 GLU A 131 REMARK 465 ASP A 132 REMARK 465 ALA A 133 REMARK 465 GLU A 134 REMARK 465 LYS A 224 REMARK 465 LYS A 225 REMARK 465 ASP A 226 REMARK 465 GLU A 227 REMARK 465 LEU A 228 REMARK 465 THR A 229 REMARK 465 LEU A 230 REMARK 465 GLU A 231 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 GLY A 125 CA C O REMARK 470 VAL A 223 CA C O CB CG1 CG2 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 117 76.02 -104.66 REMARK 500 ILE A 124 -35.42 -132.54 REMARK 500 LEU A 222 -74.04 -121.50 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 SO4 A 273 DBREF 1QDE A 8 231 UNP P10081 IF4A_YEAST 9 232 SEQRES 1 A 224 GLU GLU SER GLN ILE GLN THR ASN TYR ASP LYS VAL VAL SEQRES 2 A 224 TYR LYS PHE ASP ASP MET GLU LEU ASP GLU ASN LEU LEU SEQRES 3 A 224 ARG GLY VAL PHE GLY TYR GLY PHE GLU GLU PRO SER ALA SEQRES 4 A 224 ILE GLN GLN ARG ALA ILE MET PRO ILE ILE GLU GLY HIS SEQRES 5 A 224 ASP VAL LEU ALA GLN ALA GLN SER GLY THR GLY LYS THR SEQRES 6 A 224 GLY THR PHE SER ILE ALA ALA LEU GLN ARG ILE ASP THR SEQRES 7 A 224 SER VAL LYS ALA PRO GLN ALA LEU MET LEU ALA PRO THR SEQRES 8 A 224 ARG GLU LEU ALA LEU GLN ILE GLN LYS VAL VAL MET ALA SEQRES 9 A 224 LEU ALA PHE HIS MET ASP ILE LYS VAL HIS ALA CYS ILE SEQRES 10 A 224 GLY GLY THR SER PHE VAL GLU ASP ALA GLU GLY LEU ARG SEQRES 11 A 224 ASP ALA GLN ILE VAL VAL GLY THR PRO GLY ARG VAL PHE SEQRES 12 A 224 ASP ASN ILE GLN ARG ARG ARG PHE ARG THR ASP LYS ILE SEQRES 13 A 224 LYS MET PHE ILE LEU ASP GLU ALA ASP GLU MET LEU SER SEQRES 14 A 224 SER GLY PHE LYS GLU GLN ILE TYR GLN ILE PHE THR LEU SEQRES 15 A 224 LEU PRO PRO THR THR GLN VAL VAL LEU LEU SER ALA THR SEQRES 16 A 224 MET PRO ASN ASP VAL LEU GLU VAL THR THR LYS PHE MET SEQRES 17 A 224 ARG ASN PRO VAL ARG ILE LEU VAL LYS LYS ASP GLU LEU SEQRES 18 A 224 THR LEU GLU HET SO4 A 273 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *50(H2 O) HELIX 1 1 LYS A 22 GLU A 27 5 6 HELIX 2 2 ASP A 29 GLY A 40 1 12 HELIX 3 3 SER A 45 GLU A 57 1 13 HELIX 4 4 GLY A 70 ILE A 83 1 14 HELIX 5 5 THR A 98 ALA A 113 1 16 HELIX 6 6 THR A 145 ARG A 155 1 11 HELIX 7 7 GLU A 170 SER A 177 1 8 HELIX 8 8 PHE A 179 LEU A 190 1 12 HELIX 9 9 PRO A 204 MET A 215 1 12 SHEET 1 A 7 VAL A 120 CYS A 123 0 SHEET 2 A 7 ILE A 141 GLY A 144 1 O ILE A 141 N HIS A 121 SHEET 3 A 7 ALA A 92 LEU A 95 1 O ALA A 92 N VAL A 142 SHEET 4 A 7 MET A 165 ASP A 169 1 O MET A 165 N LEU A 93 SHEET 5 A 7 GLN A 195 SER A 200 1 O GLN A 195 N PHE A 166 SHEET 6 A 7 VAL A 61 GLN A 64 1 O VAL A 61 N LEU A 198 SHEET 7 A 7 VAL A 219 ILE A 221 1 O VAL A 219 N LEU A 62 SITE 1 AC1 5 GLY A 68 THR A 69 GLY A 70 LYS A 71 SITE 2 AC1 5 THR A 72 CRYST1 38.880 59.280 92.050 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 0.025720 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010864 0.00000