HEADER TRANSLATION 05-JUL-98 1BKB TITLE INITIATION FACTOR 5A FROM ARCHEBACTERIUM PYROBACULUM AEROPHILUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATION INITIATION FACTOR 5A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: MSE HAS REPLACED MET, AS SELENO-METHIONINE WAS COMPND 7 INCORPORATED INTO THE PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROBACULUM AEROPHILUM; SOURCE 3 ORGANISM_TAXID: 13773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS TRANSLATION INITIATION FACTOR, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR T.S.PEAT,J.NEWMAN,G.S.WALDO,J.BERENDZEN,T.C.TERWILLIGER REVDAT 5 30-OCT-24 1BKB 1 SEQADV LINK REVDAT 4 24-FEB-09 1BKB 1 VERSN REVDAT 3 22-DEC-99 1BKB 1 HEADER COMPND REVDAT 2 18-NOV-98 1BKB 1 SOURCE COMPND REMARK JRNL REVDAT 2 2 1 KEYWDS HEADER MODRES REVDAT 1 04-NOV-98 1BKB 0 JRNL AUTH T.S.PEAT,J.NEWMAN,G.S.WALDO,J.BERENDZEN,T.C.TERWILLIGER JRNL TITL STRUCTURE OF TRANSLATION INITIATION FACTOR 5A FROM JRNL TITL 2 PYROBACULUM AEROPHILUM AT 1.75 A RESOLUTION. JRNL REF STRUCTURE V. 6 1207 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9753699 JRNL DOI 10.1016/S0969-2126(98)00120-8 REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21532 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 : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1052 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2507 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 153 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1062 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.20000 REMARK 3 B22 (A**2) : 3.20000 REMARK 3 B33 (A**2) : -6.40000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 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) : 0.640 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.130 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.410 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.730 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : COMBINATION REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 110.6 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: ALTHOUGH AN ANOMALOUS PARAMETER FILE REMARK 3 SHOULD HAVE BEEN USED IN REFINEMENT (SE ATOMS IN STRUCTURE), REMARK 3 THIS WAS NOT DONE. DATA CUTOFF HIGH (ABS(F)) : 1392611.86 DATA REMARK 3 CUTOFF LOW (ABS(F)) : 0.00 REMARK 4 REMARK 4 1BKB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171855. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21532 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : 0.23000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, CNS 0.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: A THREE WAVELENGTH DATA SET WAS USED TO FIND THE SELENIUM REMARK 200 POSITIONS AND PHASE THE ELECTRON DENSITY MAPS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED AT 8 DEGREES REMARK 280 IN 50MM HEPES PH 7.5, 6-8% PEG 4000, 5MM BETA- MERCAPTOETHANOL, REMARK 280 TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 57.06500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.06500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.29500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 57.06500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.06500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.29500 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 57.06500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 57.06500 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 16.29500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 57.06500 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 57.06500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 16.29500 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: TETRAMERIC 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 350 BIOMT1 2 0.000000 1.000000 0.000000 114.13000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 114.13000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 114.13000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 -114.13000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 228.26000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 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 6 -63.00 -133.29 REMARK 500 TYR A 108 34.55 -98.90 REMARK 500 LEU A 129 -125.16 58.44 REMARK 500 LYS A 138 -92.59 115.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BKB A 4 139 UNP P56635 IF5A_PYRAE 1 136 SEQADV 1BKB MSE A 7 UNP P56635 MET 4 CONFLICT SEQADV 1BKB MSE A 94 UNP P56635 MET 91 CONFLICT SEQADV 1BKB MSE A 96 UNP P56635 MET 93 CONFLICT SEQADV 1BKB MSE A 106 UNP P56635 MET 103 CONFLICT SEQRES 1 A 136 LYS TRP VAL MSE SER THR LYS TYR VAL GLU ALA GLY GLU SEQRES 2 A 136 LEU LYS GLU GLY SER TYR VAL VAL ILE ASP GLY GLU PRO SEQRES 3 A 136 CYS ARG VAL VAL GLU ILE GLU LYS SER LYS THR GLY LYS SEQRES 4 A 136 HIS GLY SER ALA LYS ALA ARG ILE VAL ALA VAL GLY VAL SEQRES 5 A 136 PHE ASP GLY GLY LYS ARG THR LEU SER LEU PRO VAL ASP SEQRES 6 A 136 ALA GLN VAL GLU VAL PRO ILE ILE GLU LYS PHE THR ALA SEQRES 7 A 136 GLN ILE LEU SER VAL SER GLY ASP VAL ILE GLN LEU MSE SEQRES 8 A 136 ASP MSE ARG ASP TYR LYS THR ILE GLU VAL PRO MSE LYS SEQRES 9 A 136 TYR VAL GLU GLU GLU ALA LYS GLY ARG LEU ALA PRO GLY SEQRES 10 A 136 ALA GLU VAL GLU VAL TRP GLN ILE LEU ASP ARG TYR LYS SEQRES 11 A 136 ILE ILE ARG VAL LYS GLY MODRES 1BKB MSE A 7 MET SELENOMETHIONINE MODRES 1BKB MSE A 94 MET SELENOMETHIONINE MODRES 1BKB MSE A 96 MET SELENOMETHIONINE MODRES 1BKB MSE A 106 MET SELENOMETHIONINE HET MSE A 7 8 HET MSE A 94 8 HET MSE A 96 8 HET MSE A 106 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 HOH *143(H2 O) HELIX 1 1 ALA A 14 GLU A 16 5 3 HELIX 2 2 GLU A 111 ARG A 116 1 6 SHEET 1 A 2 LYS A 10 GLU A 13 0 SHEET 2 A 2 GLN A 70 VAL A 73 -1 N VAL A 73 O LYS A 10 SHEET 1 B 4 TYR A 22 ILE A 25 0 SHEET 2 B 4 GLU A 28 SER A 38 -1 N CYS A 30 O VAL A 23 SHEET 3 B 4 LYS A 47 GLY A 54 -1 N VAL A 53 O ARG A 31 SHEET 4 B 4 LYS A 60 PRO A 66 -1 N LEU A 65 O ALA A 48 SHEET 1 C 3 GLU A 77 GLN A 82 0 SHEET 2 C 3 GLU A 122 ILE A 128 -1 N GLN A 127 O GLU A 77 SHEET 3 C 3 ARG A 131 VAL A 137 -1 N ARG A 136 O GLU A 124 SHEET 1 D 2 ILE A 91 LEU A 93 0 SHEET 2 D 2 ILE A 102 VAL A 104 -1 N VAL A 104 O ILE A 91 LINK C VAL A 6 N MSE A 7 1555 1555 1.33 LINK C MSE A 7 N SER A 8 1555 1555 1.33 LINK C LEU A 93 N MSE A 94 1555 1555 1.33 LINK C MSE A 94 N ASP A 95 1555 1555 1.33 LINK C ASP A 95 N MSE A 96 1555 1555 1.33 LINK C MSE A 96 N ARG A 97 1555 1555 1.33 LINK C PRO A 105 N MSE A 106 1555 1555 1.33 LINK C MSE A 106 N LYS A 107 1555 1555 1.33 CRYST1 114.130 114.130 32.590 90.00 90.00 90.00 I 4 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 0.008762 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030684 0.00000