PDB Short entry for 2IX8 HEADER NUCLEOTIDE-BINDING 07-JUL-06 2IX8 TITLE MODEL FOR EEF3 BOUND TO AN 80S RIBOSOME CAVEAT 2IX8 GLU A 1237 C-ALPHA IS PLANAR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELONGATION FACTOR 3A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-976; COMPND 5 SYNONYM: EF-3A, EF-3, TRANSLATION ELONGATION FACTOR 3A, EUKARYOTIC COMPND 6 ELONGATION FACTOR 3, EEF3, YEAST ELONGATION FACTOR 3; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: TRANSLATION ELONGATION IN FUNGI ABC-TYPE ATPASE TRNA COMPND 9 RELEASE 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: SACCHAROMYCES CEREVISIAE; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: WCGA; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PYES2.1-TOPO KEYWDS NUCLEOTIDE-BINDING, PROTEIN BIOSYNTHESIS, PHOSPHORYLATION, ELONGATION KEYWDS 2 FACTOR, RNA-BINDING, ATP-BINDING, RRNA-BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR C.B.F.ANDERSEN,T.BECKER,M.BLAU,M.ANAND,M.HALIC,B.BALAR,T.MIELKE, AUTHOR 2 T.BOESEN,J.S.PEDERSEN,C.M.T.SPAHN,T.G.KINZY,G.R.ANDERSEN,R.BECKMANN REVDAT 5 23-AUG-17 2IX8 1 REMARK REVDAT 4 14-APR-10 2IX8 1 VERSN REVDAT 3 07-APR-09 2IX8 1 REMARK LINK CRYST1 SCALE1 REVDAT 3 2 1 SCALE2 SCALE3 CONECT MASTER REVDAT 2 24-FEB-09 2IX8 1 VERSN REVDAT 1 10-JUL-07 2IX8 0 JRNL AUTH C.B.F.ANDERSEN,T.BECKER,M.BLAU,M.ANAND,M.HALIC,B.BALAR, JRNL AUTH 2 T.MIELKE,T.BOESEN,J.S.PEDERSEN,C.M.T.SPAHN,T.G.KINZY, JRNL AUTH 3 G.R.ANDERSEN,R.BECKMANN JRNL TITL STRUCTURE OF EEF3 AND THE MECHANISM OF TRANSFER RNA RELEASE JRNL TITL 2 FROM THE E-SITE. JRNL REF NATURE V. 443 663 2006 JRNL REFN ISSN 0028-0836 JRNL PMID 16929303 JRNL DOI 10.1038/NATURE05126 REMARK 2 REMARK 2 RESOLUTION. 6.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : O, SITUS, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 9.900 REMARK 3 NUMBER OF PARTICLES : 37700 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 2IX8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290029285. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : 80S-RNC-EEF3-AMP-PNP COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.17 REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : LIQUID ETHANE REMARK 245 SAMPLE BUFFER : 20MM HEPES,PH 7.5,10MM REMARK 245 MG(OAC)2,150MM KOAC 1MM DTT, REMARK 245 0.05% NIKKOL, 125MM SUCROSE, REMARK 245 0.01MG -ML-1 CYCLOHEXIMIDE, REMARK 245 0.5MM AMP-PNP,0.1MM NEOMYCIN, REMARK 245 0.3% DESOXYBIGCHAPS REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 11-FEB-05 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 95.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 20.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 39000 REMARK 245 CALIBRATED MAGNIFICATION : 38900 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 GLU A1763 CA C O CB CG CD OE1 REMARK 470 GLU A1763 OE2 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 CA GLN A 1865 NE2 GLN A 1912 0.18 REMARK 500 O GLU A 1206 CA ILE A 1209 0.24 REMARK 500 ND2 ASN A 1778 N ALA A 1782 0.29 REMARK 500 N VAL A 1319 N GLY A 1320 0.33 REMARK 500 N GLY A 1762 CG ARG A 1765 0.38 REMARK 500 CZ TYR A 1439 N GLY A 1895 0.43 REMARK 500 CE LYS A 1442 CD1 ILE A 1887 0.44 REMARK 500 CG2 THR A 1233 CB ALA A 1438 0.51 REMARK 500 CG LEU A 1165 C ALA A 1369 0.52 REMARK 500 CB ASP A 1422 NH1 ARG A 1451 0.53 REMARK 500 CD2 LEU A 1165 O ALA A 1369 0.54 REMARK 500 CA GLU A 1766 NH1 ARG A 1770 0.62 REMARK 500 CA GLN A 1280 CD2 LEU A 1331 0.65 REMARK 500 N ALA A 1164 OD1 ASP A 1370 0.65 REMARK 500 CE LYS A 1661 OG SER A 1693 0.68 REMARK 500 O ARG A 1758 N THR A 1761 0.69 REMARK 500 CG LEU A 1861 CD GLN A 1865 0.71 REMARK 500 O GLY A 1230 CA ALA A 1231 0.71 REMARK 500 C ALA A 1124 CE2 TYR A 1363 0.72 REMARK 500 O ALA A 1124 CE2 TYR A 1363 0.74 REMARK 500 C GLY A 1864 CG GLN A 1912 0.74 REMARK 500 O ARG A 1765 CD ARG A 1770 0.75 REMARK 500 O ARG A 1318 N ASN A 1321 0.76 REMARK 500 OD1 ASN A 1464 CD LYS A 1903 0.76 REMARK 500 C LYS A 1160 OE1 GLU A 1374 0.76 REMARK 500 CA GLY A 1842 O GLU A 1843 0.78 REMARK 500 C GLU A 1206 N ILE A 1209 0.79 REMARK 500 OD2 ASP A 1422 CD ARG A 1451 0.80 REMARK 500 CA GLY A 1864 CD GLN A 1912 0.81 REMARK 500 C GLY A 1427 CA GLU A 1428 0.83 REMARK 500 C GLN A 1865 CD GLN A 1912 0.83 REMARK 500 CE2 TYR A 1620 CE1 PHE A 1627 0.85 REMARK 500 CD1 TYR A 1811 SE MSE A 1851 0.85 REMARK 500 O ASN A 1121 OH TYR A 1389 0.86 REMARK 500 O HIS A 1333 OG1 THR A 1339 0.87 REMARK 500 CB ALA A 1124 CE1 TYR A 1389 0.89 REMARK 500 OH TYR A 1439 C ARG A 1894 0.89 REMARK 500 C GLY A 1864 CB GLN A 1912 0.89 REMARK 500 CZ TYR A 1620 CE1 PHE A 1627 0.90 REMARK 500 C HIS A 1333 OG1 THR A 1339 0.90 REMARK 500 CA GLY A 1864 CG GLN A 1912 0.91 REMARK 500 OD1 ASN A 1464 CE LYS A 1903 0.91 REMARK 500 CB GLN A 1280 CG LEU A 1331 0.91 REMARK 500 CG ASN A 1778 CA ALA A 1782 0.91 REMARK 500 CG GLN A 1280 N LEU A 1331 0.92 REMARK 500 O LYS A 1661 OG SER A 1691 0.92 REMARK 500 N GLY A 1864 NE2 GLN A 1912 0.93 REMARK 500 CB ASP A 1422 CZ ARG A 1451 0.94 REMARK 500 OE2 GLU A 1646 NZ LYS A 1936 0.94 REMARK 500 O GLN A 1865 CD GLN A 1912 0.97 REMARK 500 REMARK 500 THIS ENTRY HAS 583 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MSE A1193 CB MSE A1193 CG 1.394 REMARK 500 THR A1194 CB THR A1194 CG2 1.017 REMARK 500 LYS A1195 CB LYS A1195 CG 0.329 REMARK 500 THR A1197 CB THR A1197 OG1 0.377 REMARK 500 THR A1197 CB THR A1197 CG2 0.910 REMARK 500 ALA A1236 C GLU A1237 N -0.351 REMARK 500 VAL A1238 CB VAL A1238 CG1 0.366 REMARK 500 VAL A1238 CB VAL A1238 CG2 0.137 REMARK 500 THR A1239 CB THR A1239 OG1 0.561 REMARK 500 THR A1239 CB THR A1239 CG2 0.379 REMARK 500 PRO A1240 CD PRO A1240 N 0.133 REMARK 500 ALA A1241 C THR A1242 N -0.716 REMARK 500 LEU A1869 C LEU A1869 O 15.557 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 ALA A1192 CA - C - N ANGL. DEV. = -37.1 DEGREES REMARK 500 ALA A1192 O - C - N ANGL. DEV. = 33.7 DEGREES REMARK 500 MSE A1193 C - N - CA ANGL. DEV. = -15.2 DEGREES REMARK 500 MSE A1193 CA - CB - CG ANGL. DEV. = -36.0 DEGREES REMARK 500 THR A1194 OG1 - CB - CG2 ANGL. DEV. = -41.7 DEGREES REMARK 500 THR A1194 CA - CB - OG1 ANGL. DEV. = -17.2 DEGREES REMARK 500 THR A1194 CA - CB - CG2 ANGL. DEV. = -20.3 DEGREES REMARK 500 LYS A1195 CA - CB - CG ANGL. DEV. = 33.9 DEGREES REMARK 500 LYS A1195 N - CA - C ANGL. DEV. = -19.4 DEGREES REMARK 500 THR A1197 OG1 - CB - CG2 ANGL. DEV. = -42.3 DEGREES REMARK 500 THR A1197 CA - CB - OG1 ANGL. DEV. = 24.2 DEGREES REMARK 500 GLY A1230 CA - C - N ANGL. DEV. = -52.5 DEGREES REMARK 500 GLY A1230 O - C - N ANGL. DEV. = -64.6 DEGREES REMARK 500 ALA A1231 C - N - CA ANGL. DEV. = -68.3 DEGREES REMARK 500 ALA A1236 CA - C - N ANGL. DEV. = 30.1 DEGREES REMARK 500 ALA A1236 O - C - N ANGL. DEV. = -31.7 DEGREES REMARK 500 GLU A1237 C - N - CA ANGL. DEV. = 37.3 DEGREES REMARK 500 GLU A1237 CB - CA - C ANGL. DEV. = -13.1 DEGREES REMARK 500 GLU A1237 N - CA - CB ANGL. DEV. = 40.8 DEGREES REMARK 500 VAL A1238 CG1 - CB - CG2 ANGL. DEV. = -21.3 DEGREES REMARK 500 THR A1239 OG1 - CB - CG2 ANGL. DEV. = -33.6 DEGREES REMARK 500 PRO A1240 C - N - CD ANGL. DEV. = -13.0 DEGREES REMARK 500 PRO A1240 N - CA - CB ANGL. DEV. = 7.5 DEGREES REMARK 500 PRO A1240 CA - CB - CG ANGL. DEV. = -12.4 DEGREES REMARK 500 PRO A1240 N - CD - CG ANGL. DEV. = -13.9 DEGREES REMARK 500 ALA A1241 CA - C - N ANGL. DEV. = -16.2 DEGREES REMARK 500 GLY A1427 CA - C - N ANGL. DEV. = -57.0 DEGREES REMARK 500 GLY A1427 O - C - N ANGL. DEV. = -12.2 DEGREES REMARK 500 GLU A1428 C - N - CA ANGL. DEV. = -87.5 DEGREES REMARK 500 MSE A1768 CA - C - N ANGL. DEV. = -18.8 DEGREES REMARK 500 LEU A1869 CA - C - O ANGL. DEV. = 15.2 DEGREES REMARK 500 LEU A1869 O - C - N ANGL. DEV. = -41.2 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 ALA A1022 -18.05 -49.60 REMARK 500 ASP A1201 32.04 -78.27 REMARK 500 PRO A1219 -9.85 -56.66 REMARK 500 ALA A1231 2.45 158.72 REMARK 500 THR A1232 -25.69 38.42 REMARK 500 THR A1233 53.73 73.74 REMARK 500 GLU A1237 68.96 70.06 REMARK 500 ASN A1419 -151.42 -69.46 REMARK 500 GLU A1423 -36.74 -27.36 REMARK 500 ASP A1425 -153.71 31.61 REMARK 500 GLU A1426 -47.38 -169.52 REMARK 500 ALA A1438 91.34 -173.24 REMARK 500 ALA A1441 -13.61 69.29 REMARK 500 LYS A1447 80.75 64.38 REMARK 500 LEU A1450 74.76 -162.19 REMARK 500 CYS A1461 -164.70 -121.67 REMARK 500 CYS A1489 84.22 -163.82 REMARK 500 GLU A1495 -8.56 56.27 REMARK 500 ASP A1499 -134.16 -126.13 REMARK 500 SER A1506 -165.19 -79.52 REMARK 500 VAL A1516 56.81 -94.41 REMARK 500 GLU A1568 77.20 49.62 REMARK 500 VAL A1605 -92.36 -117.47 REMARK 500 CYS A1606 117.54 -32.85 REMARK 500 ASN A1611 -156.43 -71.80 REMARK 500 TYR A1612 56.30 -155.38 REMARK 500 LYS A1616 -164.34 -111.05 REMARK 500 LEU A1617 47.85 -149.56 REMARK 500 ASN A1623 -166.95 -72.94 REMARK 500 ALA A1636 69.83 -155.11 REMARK 500 ASP A1644 34.00 -85.92 REMARK 500 LEU A1645 -33.56 -140.39 REMARK 500 PHE A1649 154.60 -45.33 REMARK 500 PRO A1676 101.42 -47.73 REMARK 500 THR A1678 -151.84 -97.23 REMARK 500 SER A1691 -152.54 -114.08 REMARK 500 SER A1693 11.37 -145.05 REMARK 500 ASN A1702 -173.75 -66.23 REMARK 500 LYS A1736 -165.09 -104.17 REMARK 500 HIS A1738 -76.84 -61.67 REMARK 500 HIS A1746 37.02 -148.04 REMARK 500 MSE A1768 88.48 -162.07 REMARK 500 ASP A1769 27.96 -5.80 REMARK 500 ASN A1772 -136.74 -105.21 REMARK 500 ARG A1773 -60.56 -109.35 REMARK 500 ILE A1775 46.32 -96.34 REMARK 500 ASN A1784 58.62 -91.56 REMARK 500 GLU A1790 10.48 54.60 REMARK 500 SER A1801 -152.67 -145.89 REMARK 500 LYS A1806 -101.20 32.13 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 1236 GLU A 1237 63.96 REMARK 500 MSE A 1768 ASP A 1769 -141.53 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 GLY A1230 -19.82 REMARK 500 ALA A1241 21.24 REMARK 500 GLY A1427 30.87 REMARK 500 MSE A1768 25.29 REMARK 500 LEU A1869 -50.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1233 RELATED DB: EMDB REMARK 900 STRUCTURE OF EEF3 AND THE MECHANISM OF TRANSFER RNA RELEASE FROM REMARK 900 THE E-SITE. REMARK 999 REMARK 999 SEQUENCE REMARK 999 PDB LACKS THE C-TERMINAL PART OF EEF3 (RESIDUES 977-1044) DBREF 2IX8 A 1001 1976 UNP P16521 EF3A_YEAST 1 976 SEQRES 1 A 976 SER ASP SER GLN GLN SER ILE LYS VAL LEU GLU GLU LEU SEQRES 2 A 976 PHE GLN LYS LEU SER VAL ALA THR ALA ASP ASN ARG HIS SEQRES 3 A 976 GLU ILE ALA SER GLU VAL ALA SER PHE LEU ASN GLY ASN SEQRES 4 A 976 ILE ILE GLU HIS ASP VAL PRO GLU HIS PHE PHE GLY GLU SEQRES 5 A 976 LEU ALA LYS GLY ILE LYS ASP LYS LYS THR ALA ALA ASN SEQRES 6 A 976 ALA MSE GLN ALA VAL ALA HIS ILE ALA ASN GLN SER ASN SEQRES 7 A 976 LEU SER PRO SER VAL GLU PRO TYR ILE VAL GLN LEU VAL SEQRES 8 A 976 PRO ALA ILE CYS THR ASN ALA GLY ASN LYS ASP LYS GLU SEQRES 9 A 976 ILE GLN SER VAL ALA SER GLU THR LEU ILE SER ILE VAL SEQRES 10 A 976 ASN ALA VAL ASN PRO VAL ALA ILE LYS ALA LEU LEU PRO SEQRES 11 A 976 HIS LEU THR ASN ALA ILE VAL GLU THR ASN LYS TRP GLN SEQRES 12 A 976 GLU LYS ILE ALA ILE LEU ALA ALA PHE SER ALA MSE VAL SEQRES 13 A 976 ASP ALA ALA LYS ASP GLN VAL ALA LEU ARG MSE PRO GLU SEQRES 14 A 976 LEU ILE PRO VAL LEU SER GLU THR MSE TRP ASP THR LYS SEQRES 15 A 976 LYS GLU VAL LYS ALA ALA ALA THR ALA ALA MSE THR LYS SEQRES 16 A 976 ALA THR GLU THR VAL ASP ASN LYS ASP ILE GLU ARG PHE SEQRES 17 A 976 ILE PRO SER LEU ILE GLN CYS ILE ALA ASP PRO THR GLU SEQRES 18 A 976 VAL PRO GLU THR VAL HIS LEU LEU GLY ALA THR THR PHE SEQRES 19 A 976 VAL ALA GLU VAL THR PRO ALA THR LEU SER ILE MSE VAL SEQRES 20 A 976 PRO LEU LEU SER ARG GLY LEU ASN GLU ARG GLU THR GLY SEQRES 21 A 976 ILE LYS ARG LYS SER ALA VAL ILE ILE ASP ASN MSE CYS SEQRES 22 A 976 LYS LEU VAL GLU ASP PRO GLN VAL ILE ALA PRO PHE LEU SEQRES 23 A 976 GLY LYS LEU LEU PRO GLY LEU LYS SER ASN PHE ALA THR SEQRES 24 A 976 ILE ALA ASP PRO GLU ALA ARG GLU VAL THR LEU ARG ALA SEQRES 25 A 976 LEU LYS THR LEU ARG ARG VAL GLY ASN VAL GLY GLU ASP SEQRES 26 A 976 ASP ALA ILE PRO GLU LEU SER HIS ALA GLY ASP VAL SER SEQRES 27 A 976 THR THR LEU GLN VAL VAL ASN GLU LEU LEU LYS ASP GLU SEQRES 28 A 976 THR VAL ALA PRO ARG PHE LYS ILE VAL VAL GLU TYR ILE SEQRES 29 A 976 ALA ALA ILE GLY ALA ASP LEU ILE ASP GLU ARG ILE ILE SEQRES 30 A 976 ASP GLN GLN ALA TRP PHE THR HIS ILE THR PRO TYR MSE SEQRES 31 A 976 THR ILE PHE LEU HIS GLU LYS LYS ALA LYS ASP ILE LEU SEQRES 32 A 976 ASP GLU PHE ARG LYS ARG ALA VAL ASP ASN ILE PRO VAL SEQRES 33 A 976 GLY PRO ASN PHE ASP ASP GLU GLU ASP GLU GLY GLU ASP SEQRES 34 A 976 LEU CYS ASN CYS GLU PHE SER LEU ALA TYR GLY ALA LYS SEQRES 35 A 976 ILE LEU LEU ASN LYS THR GLN LEU ARG LEU LYS ARG ALA SEQRES 36 A 976 ARG ARG TYR GLY ILE CYS GLY PRO ASN GLY CYS GLY LYS SEQRES 37 A 976 SER THR LEU MSE ARG ALA ILE ALA ASN GLY GLN VAL ASP SEQRES 38 A 976 GLY PHE PRO THR GLN GLU GLU CYS ARG THR VAL TYR VAL SEQRES 39 A 976 GLU HIS ASP ILE ASP GLY THR HIS SER ASP THR SER VAL SEQRES 40 A 976 LEU ASP PHE VAL PHE GLU SER GLY VAL GLY THR LYS GLU SEQRES 41 A 976 ALA ILE LYS ASP LYS LEU ILE GLU PHE GLY PHE THR ASP SEQRES 42 A 976 GLU MSE ILE ALA MSE PRO ILE SER ALA LEU SER GLY GLY SEQRES 43 A 976 TRP LYS MSE LYS LEU ALA LEU ALA ARG ALA VAL LEU ARG SEQRES 44 A 976 ASN ALA ASP ILE LEU LEU LEU ASP GLU PRO THR ASN HIS SEQRES 45 A 976 LEU ASP THR VAL ASN VAL ALA TRP LEU VAL ASN TYR LEU SEQRES 46 A 976 ASN THR CYS GLY ILE THR SER ILE THR ILE SER HIS ASP SEQRES 47 A 976 SER VAL PHE LEU ASP ASN VAL CYS GLU TYR ILE ILE ASN SEQRES 48 A 976 TYR GLU GLY LEU LYS LEU ARG LYS TYR LYS GLY ASN PHE SEQRES 49 A 976 THR GLU PHE VAL LYS LYS CYS PRO ALA ALA LYS ALA TYR SEQRES 50 A 976 GLU GLU LEU SER ASN THR ASP LEU GLU PHE LYS PHE PRO SEQRES 51 A 976 GLU PRO GLY TYR LEU GLU GLY VAL LYS THR LYS GLN LYS SEQRES 52 A 976 ALA ILE VAL LYS VAL THR ASN MSE GLU PHE GLN TYR PRO SEQRES 53 A 976 GLY THR SER LYS PRO GLN ILE THR ASP ILE ASN PHE GLN SEQRES 54 A 976 CYS SER LEU SER SER ARG ILE ALA VAL ILE GLY PRO ASN SEQRES 55 A 976 GLY ALA GLY LYS SER THR LEU ILE ASN VAL LEU THR GLY SEQRES 56 A 976 GLU LEU LEU PRO THR SER GLY GLU VAL TYR THR HIS GLU SEQRES 57 A 976 ASN CYS ARG ILE ALA TYR ILE LYS GLN HIS ALA PHE ALA SEQRES 58 A 976 HIS ILE GLU SER HIS LEU ASP LYS THR PRO SER GLU TYR SEQRES 59 A 976 ILE GLN TRP ARG PHE GLN THR GLY GLU ASP ARG GLU THR SEQRES 60 A 976 MSE ASP ARG ALA ASN ARG GLN ILE ASN GLU ASN ASP ALA SEQRES 61 A 976 GLU ALA MSE ASN LYS ILE PHE LYS ILE GLU GLY THR PRO SEQRES 62 A 976 ARG ARG ILE ALA GLY ILE HIS SER ARG ARG LYS PHE LYS SEQRES 63 A 976 ASN THR TYR GLU TYR GLU CYS SER PHE LEU LEU GLY GLU SEQRES 64 A 976 ASN ILE GLY MSE LYS SER GLU ARG TRP VAL PRO MSE MSE SEQRES 65 A 976 SER VAL ASP ASN ALA TRP ILE PRO ARG GLY GLU LEU VAL SEQRES 66 A 976 GLU SER HIS SER LYS MSE VAL ALA GLU VAL ASP MSE LYS SEQRES 67 A 976 GLU ALA LEU ALA SER GLY GLN PHE ARG PRO LEU THR ARG SEQRES 68 A 976 LYS GLU ILE GLU GLU HIS CYS SER MSE LEU GLY LEU ASP SEQRES 69 A 976 PRO GLU ILE VAL SER HIS SER ARG ILE ARG GLY LEU SER SEQRES 70 A 976 GLY GLY GLN LYS VAL LYS LEU VAL LEU ALA ALA GLY THR SEQRES 71 A 976 TRP GLN ARG PRO HIS LEU ILE VAL LEU ASP GLU PRO THR SEQRES 72 A 976 ASN TYR LEU ASP ARG ASP SER LEU GLY ALA LEU SER LYS SEQRES 73 A 976 ALA LEU LYS GLU PHE GLU GLY GLY VAL ILE ILE ILE THR SEQRES 74 A 976 HIS SER ALA GLU PHE THR LYS ASN LEU THR GLU GLU VAL SEQRES 75 A 976 TRP ALA VAL LYS ASP GLY ARG MSE THR PRO SER GLY HIS SEQRES 76 A 976 ASN MODRES 2IX8 MSE A 1067 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1155 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1167 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1178 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1193 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1246 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1272 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1390 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1472 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1535 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1538 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1549 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1671 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1768 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1783 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1823 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1831 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1832 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1851 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1857 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1880 MET SELENOMETHIONINE MODRES 2IX8 MSE A 1970 MET SELENOMETHIONINE HET MSE A1067 8 HET MSE A1155 8 HET MSE A1167 8 HET MSE A1178 8 HET MSE A1193 8 HET MSE A1246 8 HET MSE A1272 8 HET MSE A1390 8 HET MSE A1472 8 HET MSE A1535 8 HET MSE A1538 8 HET MSE A1549 8 HET MSE A1671 8 HET MSE A1768 8 HET MSE A1783 8 HET MSE A1823 8 HET MSE A1831 8 HET MSE A1832 8 HET MSE A1851 8 HET MSE A1857 8 HET MSE A1880 8 HET MSE A1970 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 22(C5 H11 N O2 SE) HELIX 1 1 SER A 1001 ALA A 1020 1 20 HELIX 2 2 ASN A 1024 ASN A 1037 1 14 HELIX 3 3 PRO A 1046 LYS A 1058 1 13 HELIX 4 4 THR A 1062 ALA A 1074 1 13 HELIX 5 5 VAL A 1083 GLN A 1089 1 7 HELIX 6 6 LEU A 1090 ALA A 1098 1 9 HELIX 7 7 ASP A 1102 VAL A 1120 1 19 HELIX 8 8 ASN A 1121 VAL A 1123 5 3 HELIX 9 9 ALA A 1124 THR A 1139 1 16 HELIX 10 10 LYS A 1141 ALA A 1159 1 19 HELIX 11 11 ALA A 1159 MSE A 1178 1 20 HELIX 12 12 LYS A 1182 THR A 1197 1 16 HELIX 13 13 PHE A 1208 ASP A 1218 1 11 HELIX 14 14 GLU A 1221 LEU A 1229 1 9 HELIX 15 15 THR A 1239 ASN A 1255 1 17 HELIX 16 16 GLU A 1258 LYS A 1274 1 17 HELIX 17 17 ASP A 1278 GLY A 1287 1 10 HELIX 18 18 LEU A 1289 ILE A 1300 1 12 HELIX 19 19 ASP A 1302 VAL A 1319 1 18 HELIX 20 20 GLY A 1323 ALA A 1327 5 5 HELIX 21 21 ASP A 1336 LEU A 1348 1 13 HELIX 22 22 ALA A 1354 ARG A 1356 5 3 HELIX 23 23 PHE A 1357 GLU A 1374 1 18 HELIX 24 24 ASP A 1378 ILE A 1386 1 9 HELIX 25 25 ILE A 1386 THR A 1391 1 6 HELIX 26 26 HIS A 1395 ASP A 1412 1 18 HELIX 27 27 ASP A 1421 ASP A 1425 5 5 HELIX 28 28 GLY A 1467 ASN A 1477 1 11 HELIX 29 29 THR A 1518 GLY A 1530 1 13 HELIX 30 30 SER A 1544 ARG A 1559 1 16 HELIX 31 31 ASN A 1577 GLY A 1589 1 13 HELIX 32 32 ASP A 1598 VAL A 1605 1 8 HELIX 33 33 ASN A 1623 CYS A 1631 1 9 HELIX 34 34 PRO A 1632 ALA A 1636 5 5 HELIX 35 35 LYS A 1706 THR A 1714 1 9 HELIX 36 36 HIS A 1742 LEU A 1747 5 6 HELIX 37 37 THR A 1750 PHE A 1759 1 10 HELIX 38 38 HIS A 1848 ALA A 1860 1 13 HELIX 39 39 THR A 1870 SER A 1879 1 10 HELIX 40 40 MSE A 1880 GLY A 1882 5 3 HELIX 41 41 ASP A 1884 SER A 1889 1 6 HELIX 42 42 ARG A 1892 LEU A 1896 5 5 HELIX 43 43 SER A 1897 THR A 1910 1 14 HELIX 44 44 ASP A 1927 LEU A 1938 1 12 SHEET 1 AA 2 ASP A1429 CYS A1431 0 SHEET 2 AA 2 LEU A1452 LYS A1453 -1 O LEU A1452 N LEU A1430 SHEET 1 AB 2 GLU A1434 PHE A1435 0 SHEET 2 AB 2 THR A1448 GLN A1449 -1 O THR A1448 N PHE A1435 SHEET 1 AC 2 GLY A1459 ILE A1460 0 SHEET 2 AC 2 ILE A1609 ILE A1610 1 N ILE A1610 O GLY A1459 SHEET 1 AD 2 ILE A1563 ASP A1567 0 SHEET 2 AD 2 THR A1591 ILE A1595 1 O THR A1591 N LEU A1564 SHEET 1 AE 2 VAL A1666 MSE A1671 0 SHEET 2 AE 2 ILE A1686 CYS A1690 -1 N ILE A1686 O MSE A1671 SHEET 1 AF 4 LEU A1919 ASP A1920 0 SHEET 2 AF 4 VAL A1945 ILE A1948 1 O ILE A1946 N LEU A1919 SHEET 3 AF 4 ARG A1695 ALA A1697 1 O ILE A1696 N ILE A1947 SHEET 4 AF 4 GLU A1961 VAL A1962 1 O GLU A1961 N ALA A1697 SHEET 1 AG 2 ILE A1732 ALA A1733 0 SHEET 2 AG 2 LEU A1916 ILE A1917 0 SHEET 1 AH 2 PHE A1787 ILE A1789 0 SHEET 2 AH 2 THR A1792 ARG A1794 -1 O THR A1792 N ILE A1789 SHEET 1 AI 2 GLY A1798 ILE A1799 0 SHEET 2 AI 2 CYS A1813 SER A1814 -1 N SER A1814 O GLY A1798 SHEET 1 AJ 3 ARG A1803 PHE A1805 0 SHEET 2 AJ 3 THR A1808 TYR A1811 -1 O THR A1808 N PHE A1805 SHEET 3 AJ 3 ILE A1839 PRO A1840 -1 O ILE A1839 N TYR A1811 SHEET 1 AK 2 LEU A1816 GLU A1819 0 SHEET 2 AK 2 ARG A1827 PRO A1830 -1 O ARG A1827 N GLU A1819 LINK C ALA A1066 N MSE A1067 1555 1555 1.32 LINK C MSE A1067 N GLN A1068 1555 1555 1.33 LINK C ALA A1154 N MSE A1155 1555 1555 1.33 LINK C MSE A1155 N VAL A1156 1555 1555 1.33 LINK C ARG A1166 N MSE A1167 1555 1555 1.33 LINK C MSE A1167 N PRO A1168 1555 1555 1.34 LINK C THR A1177 N MSE A1178 1555 1555 1.33 LINK C MSE A1178 N TRP A1179 1555 1555 1.33 LINK C ALA A1192 N MSE A1193 1555 1555 1.47 LINK C MSE A1193 N THR A1194 1555 1555 1.32 LINK C ILE A1245 N MSE A1246 1555 1555 1.33 LINK C MSE A1246 N VAL A1247 1555 1555 1.33 LINK C ASN A1271 N MSE A1272 1555 1555 1.33 LINK C MSE A1272 N CYS A1273 1555 1555 1.33 LINK C TYR A1389 N MSE A1390 1555 1555 1.33 LINK C MSE A1390 N THR A1391 1555 1555 1.33 LINK C LEU A1471 N MSE A1472 1555 1555 1.33 LINK C MSE A1472 N ARG A1473 1555 1555 1.33 LINK C GLU A1534 N MSE A1535 1555 1555 1.33 LINK C MSE A1535 N ILE A1536 1555 1555 1.33 LINK C ALA A1537 N MSE A1538 1555 1555 1.33 LINK C MSE A1538 N PRO A1539 1555 1555 1.35 LINK C LYS A1548 N MSE A1549 1555 1555 1.33 LINK C MSE A1549 N LYS A1550 1555 1555 1.33 LINK C ASN A1670 N MSE A1671 1555 1555 1.33 LINK C MSE A1671 N GLU A1672 1555 1555 1.33 LINK C THR A1767 N MSE A1768 1555 1555 1.33 LINK O MSE A1768 N ARG A1770 1555 1555 1.76 LINK CE MSE A1768 OD2 ASP A1856 1555 1555 1.72 LINK C MSE A1768 N ASP A1769 1555 1555 1.42 LINK OE1 GLU A1777 CG MSE A1783 1555 1555 1.69 LINK C ALA A1782 N MSE A1783 1555 1555 1.33 LINK C MSE A1783 N ASN A1784 1555 1555 1.33 LINK CB ARG A1802 CE MSE A1851 1555 1555 1.35 LINK CE1 TYR A1811 SE MSE A1851 1555 1555 1.53 LINK CE1 TYR A1811 CB MSE A1851 1555 1555 1.76 LINK CE1 TYR A1811 CG MSE A1851 1555 1555 1.35 LINK C GLY A1822 N MSE A1823 1555 1555 1.33 LINK C MSE A1823 N LYS A1824 1555 1555 1.33 LINK C PRO A1830 N MSE A1831 1555 1555 1.33 LINK C MSE A1831 N MSE A1832 1555 1555 1.33 LINK C MSE A1832 N SER A1833 1555 1555 1.33 LINK C LYS A1850 N MSE A1851 1555 1555 1.33 LINK C MSE A1851 N VAL A1852 1555 1555 1.33 LINK C ASP A1856 N MSE A1857 1555 1555 1.33 LINK C MSE A1857 N LYS A1858 1555 1555 1.33 LINK C SER A1879 N MSE A1880 1555 1555 1.33 LINK C MSE A1880 N LEU A1881 1555 1555 1.33 LINK C ARG A1969 N MSE A1970 1555 1555 1.33 LINK C MSE A1970 N THR A1971 1555 1555 1.33 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