PDB Short entry for 1QVA HEADER GENE REGULATION 07-JUL-99 1QVA TITLE YEAST INITIATION FACTOR 4A N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INITIATION FACTOR 4A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-224; COMPND 5 SYNONYM: EIF-4A, STIMULATOR FACTOR I 37, KD COMPONENT; 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: PET KEYWDS RNA HELICASE, DEAD BOX, EIF4A, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR E.R.JOHNSON,D.B.MCKAY REVDAT 4 14-FEB-24 1QVA 1 REMARK REVDAT 3 24-FEB-09 1QVA 1 VERSN REVDAT 2 01-APR-03 1QVA 1 JRNL REVDAT 1 02-DEC-99 1QVA 0 JRNL AUTH E.R.JOHNSON,D.B.MCKAY JRNL TITL CRYSTALLOGRAPHIC STRUCTURE OF THE AMINO TERMINAL DOMAIN OF JRNL TITL 2 YEAST INITIATION FACTOR 4A, A REPRESENTATIVE DEAD-BOX RNA JRNL TITL 3 HELICASE JRNL REF RNA V. 5 1526 1999 JRNL REFN ISSN 1355-8382 JRNL PMID 10606264 JRNL DOI 10.1017/S1355838299991410 REMARK 2 REMARK 2 RESOLUTION. 2.50 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, KONNERT & HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 415484.080 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 8026 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) : 0.223 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 830 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 952 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 114 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1643 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.67000 REMARK 3 B22 (A**2) : -5.77000 REMARK 3 B33 (A**2) : 17.44000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.28 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) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 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) : 1.170 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.930 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.770 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.570 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 50.24 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 : TOPPAR_EJ:PROTEIN_REP.PAR REMARK 3 PARAMETER FILE 2 : TOPPAR_EJ:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPPAR_EJ:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : TOPPAR_EJ:WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE SIDECHAINS OF THE FOLLOWING RESIDUES WERE NOT OBSERVED IN THE REMARK 3 ELECTRON REMARK 3 DENSITY AND ARE MODELED AS ALA: REMARK 3 GLN 11, ARG 137, GLN 154, ARG 156, ARG 157, ARG 159 REMARK 4 REMARK 4 1QVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009300. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : QUANTUM IV CCD SOFTWARE REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8094 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.14600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POLYETHYLENE GLYCOL, POTASSIUM REMARK 280 ACETATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 19.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.15000 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 SER A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 REMARK 465 ILE A 4 REMARK 465 THR A 5 REMARK 465 ASP A 6 REMARK 465 ILE A 7 REMARK 465 GLU A 8 REMARK 465 GLU A 9 REMARK 465 SER A 10 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 GLN A 11 CG CD OE1 NE2 REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 154 CG CD OE1 NE2 REMARK 470 ARG A 156 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 157 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 159 CG CD NE CZ NH1 NH2 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 GLN A 17 34.17 -95.96 REMARK 500 THR A 85 -32.63 -35.89 REMARK 500 VAL A 87 104.98 -57.55 REMARK 500 ILE A 124 -161.63 -129.47 REMARK 500 ASN A 205 -58.26 -29.60 REMARK 500 ASN A 217 64.79 28.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QVA A 1 223 UNP P10081 IF4A_YEAST 2 224 SEQADV 1QVA GLN A 17 UNP P10081 ASP 18 CONFLICT SEQADV 1QVA GLN A 31 UNP P10081 ASN 32 CONFLICT SEQRES 1 A 223 SER GLU GLY ILE THR ASP ILE GLU GLU SER GLN ILE GLN SEQRES 2 A 223 THR ASN TYR GLN LYS VAL VAL TYR LYS PHE ASP ASP MET SEQRES 3 A 223 GLU LEU ASP GLU GLN LEU LEU ARG GLY VAL PHE GLY TYR SEQRES 4 A 223 GLY PHE GLU GLU PRO SER ALA ILE GLN GLN ARG ALA ILE SEQRES 5 A 223 MET PRO ILE ILE GLU GLY HIS ASP VAL LEU ALA GLN ALA SEQRES 6 A 223 GLN SER GLY THR GLY LYS THR GLY THR PHE SER ILE ALA SEQRES 7 A 223 ALA LEU GLN ARG ILE ASP THR SER VAL LYS ALA PRO GLN SEQRES 8 A 223 ALA LEU MET LEU ALA PRO THR ARG GLU LEU ALA LEU GLN SEQRES 9 A 223 ILE GLN LYS VAL VAL MET ALA LEU ALA PHE HIS MET ASP SEQRES 10 A 223 ILE LYS VAL HIS ALA CYS ILE GLY GLY THR SER PHE VAL SEQRES 11 A 223 GLU ASP ALA GLU GLY LEU ARG ASP ALA GLN ILE VAL VAL SEQRES 12 A 223 GLY THR PRO GLY ARG VAL PHE ASP ASN ILE GLN ARG ARG SEQRES 13 A 223 ARG PHE ARG THR ASP LYS ILE LYS MET PHE ILE LEU ASP SEQRES 14 A 223 GLU ALA ASP GLU MET LEU SER SER GLY PHE LYS GLU GLN SEQRES 15 A 223 ILE TYR GLN ILE PHE THR LEU LEU PRO PRO THR THR GLN SEQRES 16 A 223 VAL VAL LEU LEU SER ALA THR MET PRO ASN ASP VAL LEU SEQRES 17 A 223 GLU VAL THR THR LYS PHE MET ARG ASN PRO VAL ARG ILE SEQRES 18 A 223 LEU VAL FORMUL 2 HOH *55(H2 O) HELIX 1 1 LYS A 22 MET A 26 5 5 HELIX 2 2 ASP A 29 TYR A 39 1 11 HELIX 3 3 ILE A 47 GLU A 57 1 11 HELIX 4 4 GLY A 68 ILE A 83 1 16 HELIX 5 5 THR A 98 ALA A 113 1 16 HELIX 6 6 SER A 128 ALA A 139 1 12 HELIX 7 7 THR A 145 GLN A 154 1 10 HELIX 8 8 GLU A 170 SER A 176 1 7 HELIX 9 9 PHE A 179 LEU A 189 1 11 HELIX 10 10 PRO A 204 MET A 215 1 12 SHEET 1 A 8 GLN A 13 THR A 14 0 SHEET 2 A 8 VAL A 219 LEU A 222 -1 N LEU A 222 O GLN A 13 SHEET 3 A 8 VAL A 61 GLN A 64 1 O LEU A 62 N ILE A 221 SHEET 4 A 8 GLN A 195 SER A 200 1 O VAL A 196 N VAL A 61 SHEET 5 A 8 MET A 165 LEU A 168 1 O PHE A 166 N VAL A 197 SHEET 6 A 8 ALA A 92 LEU A 95 1 O LEU A 93 N ILE A 167 SHEET 7 A 8 ILE A 141 GLY A 144 1 O VAL A 142 N MET A 94 SHEET 8 A 8 VAL A 120 CYS A 123 1 O HIS A 121 N VAL A 143 CRYST1 38.800 74.300 81.000 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 0.025773 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012346 0.00000