HEADER TRANSLATION 20-NOV-06 2NXU TITLE ATOMIC STRUCTURE OF TRANSLATION INITIATION FACTOR AIF2 BETA-SUBUNIT TITLE 2 FROM ARCHAEBACTERIA SULFOLOBUS SOLFATARICUS: HIGH RESOLUTION NMR IN TITLE 3 SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EIF-2-BETA, AIF2-BETA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 273057; SOURCE 4 STRAIN: P2; SOURCE 5 GENE: EIF2B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28B(+) KEYWDS TRANSLATION INITIATION FACTOR, ARCHAEA, AIF2BETA, TRANSLATION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR F.VASILE,E.PECHKOVA,E.STOLBOUSHKINA,M.GARBER,C.NICOLINI REVDAT 5 27-DEC-23 2NXU 1 REMARK SEQADV REVDAT 4 13-JUL-11 2NXU 1 VERSN REVDAT 3 24-FEB-09 2NXU 1 VERSN REVDAT 2 05-FEB-08 2NXU 1 JRNL REVDAT 1 30-OCT-07 2NXU 0 JRNL AUTH F.VASILE,E.PECHKOVA,C.NICOLINI JRNL TITL SOLUTION STRUCTURE OF THE BETA-SUBUNIT OF THE TRANSLATION JRNL TITL 2 INITIATION FACTOR AIF2 FROM ARCHAEBACTERIA SULFOLOBUS JRNL TITL 3 SOLFATARICUS. JRNL REF PROTEINS V. 70 1112 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 18004773 JRNL DOI 10.1002/PROT.21797 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, GROMACS 3.3.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), DAVID VAN DER SPOEL ET AL. REMARK 3 (GROMACS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WERE OBTAINED USING 635 REMARK 3 NON REDUNDANT NOE-DERIVED DISTANCE RESTRAINTS AND WERE MINIMISED REMARK 3 WITH 1000 STEPS OF CONJUGATED GRADIENT AND 1000 OF STEEPEST REMARK 3 DISCENT. FOR THE FIRST SIX RESIDUES NO SIGNALS WERE OBSERVED. REMARK 4 REMARK 4 2NXU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040436. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 8 REMARK 210 IONIC STRENGTH : 0.2 M REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : CONCENTRATION 10 MG/ML, 20 MM REMARK 210 NACL, 10% D2O IN H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3.13, DYANA 1.5 REMARK 210 METHOD USED : THE STRUCTURES WERE OBTAINED BY REMARK 210 TORSION ANGLE DYNAMIC REMARK 210 CALCULATION AND ENERGY REMARK 210 MINIMIZATION. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE TOCSY SPECTRA WERE PERFORMED WITH A MIXING TIME OF 80 REMARK 210 MS. NOESY SPECTRA WERE ACQUIRED WITH MIXING TIME OF 200 AND 300 REMARK 210 MS. FOR ALL SPECTRA WATERGATE WAS USED AS SCHEME FOR SOLVENT REMARK 210 SUPPRESSION. FOR THE FIRST SIX RESIDUES NO SIGNALS WERE OBSERVED. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 GLU A 5 REMARK 465 LYS A 6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HH22 ARG A 56 HH11 ARG A 57 1.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 3 TYR A 16 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 TYR A 51 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 5 TYR A 51 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 6 TYR A 16 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 7 TYR A 16 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 7 TYR A 51 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 8 TYR A 16 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 8 TYR A 51 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 8 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 10 TYR A 16 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 10 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES 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 1 ASP A 13 -35.41 68.59 REMARK 500 1 ARG A 14 102.73 -49.69 REMARK 500 1 SER A 17 -156.47 174.94 REMARK 500 1 LYS A 18 -76.46 62.09 REMARK 500 1 LYS A 25 144.36 68.45 REMARK 500 1 THR A 28 141.18 -171.02 REMARK 500 1 SER A 30 141.53 109.44 REMARK 500 1 LEU A 31 -84.80 95.12 REMARK 500 1 ASN A 33 78.99 0.98 REMARK 500 1 MET A 34 64.14 -100.35 REMARK 500 1 ASN A 41 -28.27 68.48 REMARK 500 1 ARG A 46 -75.64 -61.91 REMARK 500 1 ASP A 59 -65.35 -11.73 REMARK 500 1 ALA A 71 8.79 -69.64 REMARK 500 1 PRO A 73 99.00 -64.76 REMARK 500 1 ASP A 77 143.51 72.79 REMARK 500 1 ASP A 78 -141.06 -120.09 REMARK 500 1 LYS A 79 79.12 -64.49 REMARK 500 1 LYS A 87 45.15 -83.86 REMARK 500 1 SER A 90 -16.58 64.31 REMARK 500 1 GLN A 91 -154.78 -83.23 REMARK 500 1 VAL A 92 -88.68 45.66 REMARK 500 1 PHE A 100 -81.79 -71.41 REMARK 500 1 SER A 108 97.83 -56.55 REMARK 500 1 THR A 109 76.73 12.07 REMARK 500 1 LYS A 111 -86.03 61.28 REMARK 500 1 ASP A 114 46.99 -80.70 REMARK 500 1 ILE A 116 61.49 -170.11 REMARK 500 1 LYS A 118 -178.02 57.24 REMARK 500 1 GLU A 120 42.99 -68.57 REMARK 500 1 LYS A 122 72.52 33.77 REMARK 500 1 TRP A 124 -82.26 -110.30 REMARK 500 1 TYR A 125 -162.02 59.47 REMARK 500 1 CYS A 128 -144.30 52.42 REMARK 500 1 LEU A 129 -87.11 58.86 REMARK 500 1 THR A 135 71.32 61.99 REMARK 500 1 LYS A 138 147.09 59.92 REMARK 500 2 GLU A 10 107.34 -49.40 REMARK 500 2 LEU A 12 -15.58 -156.05 REMARK 500 2 ASP A 13 -19.92 78.93 REMARK 500 2 ARG A 14 101.15 -55.58 REMARK 500 2 TYR A 16 -77.54 -118.01 REMARK 500 2 LYS A 18 -47.82 69.59 REMARK 500 2 LEU A 19 105.33 -59.93 REMARK 500 2 ARG A 24 -83.30 -122.76 REMARK 500 2 LYS A 25 -146.47 61.41 REMARK 500 2 SER A 30 145.29 -177.47 REMARK 500 2 LEU A 31 -57.52 123.08 REMARK 500 2 PRO A 32 91.50 -69.04 REMARK 500 2 ASN A 33 97.44 -17.96 REMARK 500 REMARK 500 THIS ENTRY HAS 374 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 PHE A 100 0.09 SIDE CHAIN REMARK 500 1 TYR A 104 0.09 SIDE CHAIN REMARK 500 1 TYR A 125 0.07 SIDE CHAIN REMARK 500 2 TYR A 16 0.10 SIDE CHAIN REMARK 500 2 TYR A 65 0.09 SIDE CHAIN REMARK 500 2 TYR A 104 0.08 SIDE CHAIN REMARK 500 2 TYR A 125 0.11 SIDE CHAIN REMARK 500 3 TYR A 16 0.20 SIDE CHAIN REMARK 500 3 TYR A 51 0.20 SIDE CHAIN REMARK 500 3 TYR A 104 0.13 SIDE CHAIN REMARK 500 4 TYR A 16 0.10 SIDE CHAIN REMARK 500 4 TYR A 51 0.20 SIDE CHAIN REMARK 500 4 TYR A 104 0.14 SIDE CHAIN REMARK 500 5 TYR A 16 0.10 SIDE CHAIN REMARK 500 5 TYR A 51 0.09 SIDE CHAIN REMARK 500 5 TYR A 65 0.09 SIDE CHAIN REMARK 500 5 PHE A 88 0.12 SIDE CHAIN REMARK 500 6 TYR A 16 0.15 SIDE CHAIN REMARK 500 7 TYR A 16 0.20 SIDE CHAIN REMARK 500 7 TYR A 51 0.11 SIDE CHAIN REMARK 500 7 TYR A 125 0.08 SIDE CHAIN REMARK 500 8 TYR A 16 0.17 SIDE CHAIN REMARK 500 8 TYR A 51 0.13 SIDE CHAIN REMARK 500 8 TYR A 65 0.10 SIDE CHAIN REMARK 500 9 TYR A 16 0.09 SIDE CHAIN REMARK 500 9 TYR A 125 0.19 SIDE CHAIN REMARK 500 10 TYR A 16 0.12 SIDE CHAIN REMARK 500 10 TYR A 104 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 3 MET A 11 -12.77 REMARK 500 4 LEU A 66 -10.69 REMARK 500 5 LYS A 25 10.02 REMARK 500 7 SER A 112 10.50 REMARK 500 9 ALA A 103 -10.36 REMARK 500 10 LYS A 25 11.10 REMARK 500 10 ALA A 103 -10.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 2NXU A 3 140 UNP Q97W59 IF2B_SULSO 2 139 SEQADV 2NXU HIS A -5 UNP Q97W59 EXPRESSION TAG SEQADV 2NXU HIS A -4 UNP Q97W59 EXPRESSION TAG SEQADV 2NXU HIS A -3 UNP Q97W59 EXPRESSION TAG SEQADV 2NXU HIS A -2 UNP Q97W59 EXPRESSION TAG SEQADV 2NXU HIS A -1 UNP Q97W59 EXPRESSION TAG SEQADV 2NXU HIS A 0 UNP Q97W59 EXPRESSION TAG SEQADV 2NXU MET A 1 UNP Q97W59 EXPRESSION TAG SEQADV 2NXU GLY A 2 UNP Q97W59 EXPRESSION TAG SEQRES 1 A 146 HIS HIS HIS HIS HIS HIS MET GLY SER SER GLU LYS GLU SEQRES 2 A 146 TYR VAL GLU MET LEU ASP ARG LEU TYR SER LYS LEU PRO SEQRES 3 A 146 GLU LYS GLY ARG LYS GLU GLY THR GLN SER LEU PRO ASN SEQRES 4 A 146 MET ILE ILE LEU ASN ILE GLY ASN THR THR ILE ILE ARG SEQRES 5 A 146 ASN PHE ALA GLU TYR CYS ASP ARG ILE ARG ARG GLU ASP SEQRES 6 A 146 LYS ILE CYS MET LYS TYR LEU LEU LYS GLU LEU ALA ALA SEQRES 7 A 146 PRO GLY ASN VAL ASP ASP LYS GLY GLU LEU VAL ILE GLN SEQRES 8 A 146 GLY LYS PHE SER SER GLN VAL ILE ASN THR LEU MET GLU SEQRES 9 A 146 ARG PHE LEU LYS ALA TYR VAL GLU CYS SER THR CYS LYS SEQRES 10 A 146 SER LEU ASP THR ILE LEU LYS LYS GLU LYS LYS SER TRP SEQRES 11 A 146 TYR ILE VAL CYS LEU ALA CYS GLY ALA GLN THR PRO VAL SEQRES 12 A 146 LYS PRO LEU HELIX 1 1 ASN A 47 ARG A 56 1 10 HELIX 2 2 GLU A 58 GLU A 69 1 12 HELIX 3 3 VAL A 92 PHE A 100 1 9 HELIX 4 4 LYS A 102 CYS A 107 1 6 SHEET 1 A 3 LEU A 37 ASN A 38 0 SHEET 2 A 3 THR A 42 ILE A 45 -1 O ILE A 44 N LEU A 37 SHEET 3 A 3 LEU A 82 GLN A 85 -1 O ILE A 84 N THR A 43 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1