HEADER TRANSLATION 01-AUG-03 1Q46 TITLE CRYSTAL STRUCTURE OF THE EIF2 ALPHA SUBUNIT FROM SACCHAROMYCES TITLE 2 CEREVISIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATION INITIATION FACTOR 2 ALPHA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL TWO THIRDS OF EIF2A; COMPND 5 SYNONYM: EIF-2- ALPHA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS INITIATION FACTOR, EIF2, TRANSLATION, PHOSPHORYLATION SITE EXPDTA X-RAY DIFFRACTION AUTHOR S.DHALIWAL,D.W.HOFFMAN REVDAT 5 03-APR-24 1Q46 1 REMARK REVDAT 4 14-FEB-24 1Q46 1 REMARK REVDAT 3 24-FEB-09 1Q46 1 VERSN REVDAT 2 30-DEC-03 1Q46 1 JRNL REVDAT 1 28-OCT-03 1Q46 0 JRNL AUTH S.DHALIWAL,D.W.HOFFMAN JRNL TITL THE CRYSTAL STRUCTURE OF THE N-TERMINAL REGION OF THE ALPHA JRNL TITL 2 SUBUNIT OF TRANSLATION INITIATION FACTOR 2 (EIF2ALPHA) FROM JRNL TITL 3 SACCHAROMYCES CEREVISIAE PROVIDES A VIEW OF THE LOOP JRNL TITL 4 CONTAINING SERINE 51, THE TARGET OF THE EIF2ALPHA-SPECIFIC JRNL TITL 5 KINASES. JRNL REF J.MOL.BIOL. V. 334 187 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 14607111 JRNL DOI 10.1016/J.JMB.2003.09.045 REMARK 2 REMARK 2 RESOLUTION. 2.86 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) : 2.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8830 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 471 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) : 2.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.96 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 : 1441 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.216 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 1Q46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000019893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.6 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) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIUM MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8830 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.860 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 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) : 2.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58300 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: HUMAN EIF2 ALPHA SUBUNIT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE (PH=4.6), 1.8-2.5 REMARK 280 M SODIUM FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K, PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 40.59900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.00450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.00450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.89850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.00450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.00450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.29950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.00450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.00450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.89850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.00450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.00450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.29950 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 40.59900 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 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 16 -0.17 80.25 REMARK 500 SER A 57 58.09 165.79 REMARK 500 GLN A 59 -5.98 -49.36 REMARK 500 ILE A 129 -78.08 -119.44 REMARK 500 ASP A 150 111.34 -161.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 1Q46 A 1 175 UNP P20459 IF2A_YEAST 2 176 SEQRES 1 A 175 SER THR SER HIS CYS ARG PHE TYR GLU ASN LYS TYR PRO SEQRES 2 A 175 GLU ILE ASP ASP ILE VAL MET VAL ASN VAL GLN GLN ILE SEQRES 3 A 175 ALA GLU MET GLY ALA TYR VAL LYS LEU LEU GLU TYR ASP SEQRES 4 A 175 ASN ILE GLU GLY MET ILE LEU LEU SER GLU LEU SER ARG SEQRES 5 A 175 ARG ARG ILE ARG SER ILE GLN LYS LEU ILE ARG VAL GLY SEQRES 6 A 175 LYS ASN ASP VAL ALA VAL VAL LEU ARG VAL ASP LYS GLU SEQRES 7 A 175 LYS GLY TYR ILE ASP LEU SER LYS ARG ARG VAL SER SER SEQRES 8 A 175 GLU ASP ILE ILE LYS CYS GLU GLU LYS TYR GLN LYS SER SEQRES 9 A 175 LYS THR VAL HIS SER ILE LEU ARG TYR CYS ALA GLU LYS SEQRES 10 A 175 PHE GLN ILE PRO LEU GLU GLU LEU TYR LYS THR ILE ALA SEQRES 11 A 175 TRP PRO LEU SER ARG LYS PHE GLY HIS ALA TYR GLU ALA SEQRES 12 A 175 PHE LYS LEU SER ILE ILE ASP GLU THR VAL TRP GLU GLY SEQRES 13 A 175 ILE GLU PRO PRO SER LYS ASP VAL LEU ASP GLU LEU LYS SEQRES 14 A 175 ASN TYR ILE SER LYS ARG HELIX 1 1 SER A 48 LEU A 50 5 3 HELIX 2 2 SER A 57 LEU A 61 5 5 HELIX 3 3 SER A 90 PHE A 118 1 29 HELIX 4 4 PRO A 121 ILE A 129 1 9 HELIX 5 5 ILE A 129 GLY A 138 1 10 HELIX 6 6 HIS A 139 ASP A 150 1 12 HELIX 7 7 GLU A 151 GLU A 155 5 5 HELIX 8 8 SER A 161 LYS A 174 1 14 SHEET 1 A 6 ILE A 18 ILE A 26 0 SHEET 2 A 6 GLY A 30 LEU A 35 -1 O TYR A 32 N GLN A 25 SHEET 3 A 6 GLU A 42 LEU A 46 -1 O GLY A 43 N VAL A 33 SHEET 4 A 6 TYR A 81 SER A 85 1 O ILE A 82 N MET A 44 SHEET 5 A 6 ASN A 67 ASP A 76 -1 N ASP A 76 O TYR A 81 SHEET 6 A 6 ILE A 18 ILE A 26 -1 N VAL A 21 O ASP A 68 CRYST1 94.009 94.009 81.198 90.00 90.00 90.00 P 43 21 2 8 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 0.010637 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010637 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012316 0.00000