HEADER GENE REGULATION 12-OCT-98 2EIF TITLE EUKARYOTIC TRANSLATION INITIATION FACTOR 5A FROM METHANOCOCCUS TITLE 2 JANNASCHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (EUKARYOTIC TRANSLATION INITIATION FACTOR 5A); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IF-5A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 243232; SOURCE 4 STRAIN: DSM 2661; 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_PLASMID: PET21A/PSJS1240 KEYWDS EIF-5A, TRANSLATION, OB-FOLD, STRUCTURAL GENOMICS, BSGC STRUCTURE KEYWDS 2 FUNDED BY NIH, PROTEIN STRUCTURE INITIATIVE, PSI, BERKELEY KEYWDS 3 STRUCTURAL GENOMICS CENTER, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR K.K.KIM,L.W.HUNG,R.KIM,S.H.KIM,BERKELEY STRUCTURAL GENOMICS CENTER AUTHOR 2 (BSGC) REVDAT 8 23-AUG-23 2EIF 1 SEQADV REVDAT 7 13-JUL-11 2EIF 1 VERSN REVDAT 6 24-FEB-09 2EIF 1 VERSN REVDAT 5 02-JAN-07 2EIF 1 KEYWDS REMARK DBREF SEQADV REVDAT 5 2 1 MASTER REVDAT 4 25-JAN-05 2EIF 1 AUTHOR KEYWDS REMARK REVDAT 3 24-AUG-04 2EIF 1 KEYWDS REMARK REVDAT 2 29-DEC-99 2EIF 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 12-OCT-99 2EIF 0 JRNL AUTH K.K.KIM,L.W.HUNG,H.YOKOTA,R.KIM,S.H.KIM JRNL TITL CRYSTAL STRUCTURES OF EUKARYOTIC TRANSLATION INITIATION JRNL TITL 2 FACTOR 5A FROM METHANOCOCCUS JANNASCHII AT 1.8 A RESOLUTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 95 10419 1998 JRNL REFN ISSN 0027-8424 JRNL PMID 9724718 JRNL DOI 10.1073/PNAS.95.18.10419 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.K.KIM,H.YOKOTA,R.KIM,S.H.KIM REMARK 1 TITL CLONING, EXPRESSION, AND CRYSTALLIZATION OF A REMARK 1 TITL 2 HYPERTHERMOPHILIC PROTEIN THAT IS HOMOLOGOUS TO THE REMARK 1 TITL 3 EUKARYOTIC TRANSLATION INITIATION FACTOR, EIF5A REMARK 1 REF PROTEIN SCI. V. 6 2268 1997 REMARK 1 REFN ISSN 0961-8368 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 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) (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 11482 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) : 0.214 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1185 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1621 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 218 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 992 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.74000 REMARK 3 B22 (A**2) : -4.14000 REMARK 3 B33 (A**2) : -0.60000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.88000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 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) : 3.020 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.060 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 21.030; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 14.800; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 48.90 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EIF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000008406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-97; NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL; NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; N REMARK 200 RADIATION SOURCE : NSLS; NSLS; ROTATING ANODE REMARK 200 BEAMLINE : X4A; X12B; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL; NULL; 1.54 REMARK 200 MONOCHROMATOR : NULL; NULL; NULL REMARK 200 OPTICS : MSC FOCUSING MIRROR; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; NULL; NULL REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC; NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11659 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 1.980 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.23300 REMARK 200 R SYM FOR SHELL (I) : 0.23300 REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: 1EIF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL (PH 8.5), 0.2M MGCL2, REMARK 280 30% PEG4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.24150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.09900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.24150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.09900 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 GLY A 133 REMARK 465 GLY A 134 REMARK 465 LYS A 135 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 MET A 0 CG SD CE REMARK 470 VAL A 1 CG1 CG2 REMARK 470 ILE A 2 CG1 CG2 CD1 REMARK 470 ILE A 3 CG1 CG2 CD1 REMARK 470 MET A 4 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 210 O HOH A 220 2.12 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 VAL A 1 144.37 65.98 REMARK 500 MET A 4 142.77 -35.64 REMARK 500 LYS A 40 -1.45 175.53 REMARK 500 VAL A 123 42.93 38.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BSGCAIR30508 RELATED DB: TARGETDB DBREF 2EIF A 0 135 UNP Q58625 IF5A_METJA 1 132 SEQADV 2EIF MET A 0 UNP Q58625 CLONING ARTIFACT SEQADV 2EIF VAL A 1 UNP Q58625 CLONING ARTIFACT SEQADV 2EIF ILE A 2 UNP Q58625 CLONING ARTIFACT SEQADV 2EIF ILE A 3 UNP Q58625 CLONING ARTIFACT SEQRES 1 A 136 MET VAL ILE ILE MET PRO GLY THR LYS GLN VAL ASN VAL SEQRES 2 A 136 GLY SER LEU LYS VAL GLY GLN TYR VAL MET ILE ASP GLY SEQRES 3 A 136 VAL PRO CYS GLU ILE VAL ASP ILE SER VAL SER LYS PRO SEQRES 4 A 136 GLY LYS HIS GLY GLY ALA LYS ALA ARG VAL VAL GLY ILE SEQRES 5 A 136 GLY ILE PHE GLU LYS VAL LYS LYS GLU PHE VAL ALA PRO SEQRES 6 A 136 THR SER SER LYS VAL GLU VAL PRO ILE ILE ASP ARG ARG SEQRES 7 A 136 LYS GLY GLN VAL LEU ALA ILE MET GLY ASP MET VAL GLN SEQRES 8 A 136 ILE MET ASP LEU GLN THR TYR GLU THR LEU GLU LEU PRO SEQRES 9 A 136 ILE PRO GLU GLY ILE GLU GLY LEU GLU PRO GLY GLY GLU SEQRES 10 A 136 VAL GLU TYR ILE GLU ALA VAL GLY GLN TYR LYS ILE THR SEQRES 11 A 136 ARG VAL ILE GLY GLY LYS FORMUL 2 HOH *108(H2 O) HELIX 1 1 VAL A 12 SER A 14 5 3 SHEET 1 A 2 THR A 7 ASN A 11 0 SHEET 2 A 2 LYS A 68 PRO A 72 -1 N VAL A 71 O LYS A 8 SHEET 1 B 4 TYR A 20 ILE A 23 0 SHEET 2 B 4 VAL A 26 VAL A 35 -1 N CYS A 28 O VAL A 21 SHEET 3 B 4 LYS A 45 GLY A 52 -1 N ILE A 51 O GLU A 29 SHEET 4 B 4 LYS A 58 PRO A 64 -1 N ALA A 63 O ALA A 46 SHEET 1 C 5 THR A 99 PRO A 103 0 SHEET 2 C 5 MET A 88 ASP A 93 -1 N ILE A 91 O LEU A 100 SHEET 3 C 5 ILE A 74 MET A 85 -1 N MET A 85 O MET A 88 SHEET 4 C 5 GLU A 116 ALA A 122 -1 N GLU A 121 O ASP A 75 SHEET 5 C 5 GLN A 125 VAL A 131 -1 N ARG A 130 O GLU A 118 CRYST1 80.483 40.198 48.580 90.00 124.29 90.00 C 1 2 1 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 0.012425 0.000000 0.008472 0.00000 SCALE2 0.000000 0.024877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024915 0.00000