HEADER HYDROLASE/NUCLEAR PROTEIN 24-JAN-03 1OB2 TITLE E. COLI ELONGATION FACTOR EF-TU COMPLEXED WITH THE ANTIBIOTIC TITLE 2 KIRROMYCIN, A GTP ANALOG, AND PHE-TRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELONGATION FACTOR TU; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EF-TU, P-43; COMPND 5 EC: 3.6.1.48; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TRANSFER-RNA, PHE; COMPND 8 CHAIN: B; COMPND 9 OTHER_DETAILS: AMINO-ACYLATED (PHE) AT THE 3' END SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 511693; SOURCE 4 STRAIN: BL21; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 7 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 8 ORGANISM_TAXID: 4932; SOURCE 9 OTHER_DETAILS: SIGMA-ALDRICH COMPOUND KEYWDS HYDROLASE/NUCLEAR PROTEIN, HYDROLASE, GTPASE, TRANSLATION ELONGATION KEYWDS 2 FACTOR, TRANSFER RNA, HYDROLASE-NUCLEAR PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.KRISTENSEN,P.NISSEN,J.NYBORG REVDAT 8 13-DEC-23 1OB2 1 HETSYN LINK REVDAT 7 29-JUL-20 1OB2 1 COMPND REMARK HET HETNAM REVDAT 7 2 1 HETSYN FORMUL LINK SITE REVDAT 7 3 1 ATOM REVDAT 6 19-AUG-15 1OB2 1 SEQRES MODRES HET HETNAM REVDAT 6 2 1 FORMUL LINK HETATM REVDAT 5 14-NOV-12 1OB2 1 COMPND REMARK VERSN DBREF REVDAT 5 2 1 SEQADV MODRES HETSYN FORMUL REVDAT 4 24-FEB-09 1OB2 1 VERSN REVDAT 3 14-JUN-06 1OB2 1 ATOM REVDAT 2 31-AUG-04 1OB2 1 JRNL REVDAT 1 27-MAY-04 1OB2 0 JRNL AUTH R.C.NIELSEN,O.KRISTENSEN,M.KJELDGAARD,S.THIRUP,P.NISSEN JRNL TITL KIRROMYCIN DEFINES A SPECIFIC DOMAIN ARRANGEMENT OF JRNL TITL 2 ELONGATION FACTOR EF-TU JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 3.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 6224852.510 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 18794 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) : 0.220 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 963 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 3.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.56 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2928 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 162 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 : 3035 REMARK 3 NUCLEIC ACID ATOMS : 1662 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : -0.30000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.37 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.350 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) : 4.170 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.780 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.990 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.470 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 62.19 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 : TRNAPHE-MULTI.PARAM REMARK 3 PARAMETER FILE 3 : LIGANDS_HICUP.PAR REMARK 3 PARAMETER FILE 4 : MG.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : TRNAPHE-MULTI.TOP REMARK 3 TOPOLOGY FILE 3 : LIGANDS_HICUP.TOP REMARK 3 TOPOLOGY FILE 4 : MG.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT WAS INITIATED WITH X-PLOR REMARK 3 AND COMPLETED WITH CNS. ANTICODON LOOP OF TRNA IS DISORDERED AND REMARK 3 ONLY THE CHAIN TRACE IN THIS REGION IS VISIBLE IN THE ELECTRON REMARK 3 DENSITY MAPS. REMARK 4 REMARK 4 1OB2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1290012010. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : AGROVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18794 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.350 REMARK 200 RESOLUTION RANGE LOW (A) : 48.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.15400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.42900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1TTT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULPHATE, 10 MM REMARK 280 MAGNESIUM CHLORIDE, 20 MM TRIS-MES, PH 6.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+3/4,X+1/4,-Z+1/4 REMARK 290 14555 -Y+3/4,-X+3/4,-Z+3/4 REMARK 290 15555 Y+1/4,-X+1/4,Z+3/4 REMARK 290 16555 -Y+1/4,X+3/4,Z+1/4 REMARK 290 17555 X+3/4,Z+1/4,-Y+1/4 REMARK 290 18555 -X+1/4,Z+3/4,Y+1/4 REMARK 290 19555 -X+3/4,-Z+3/4,-Y+3/4 REMARK 290 20555 X+1/4,-Z+1/4,Y+3/4 REMARK 290 21555 Z+3/4,Y+1/4,-X+1/4 REMARK 290 22555 Z+1/4,-Y+1/4,X+3/4 REMARK 290 23555 -Z+1/4,Y+3/4,X+1/4 REMARK 290 24555 -Z+3/4,-Y+3/4,-X+3/4 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 98.20500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 98.20500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 98.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 98.20500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 98.20500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 98.20500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 98.20500 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 98.20500 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 98.20500 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 98.20500 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 98.20500 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 98.20500 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 98.20500 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 98.20500 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 98.20500 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 98.20500 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 98.20500 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 98.20500 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 147.30750 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 49.10250 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 49.10250 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 147.30750 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 147.30750 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 147.30750 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 49.10250 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 49.10250 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 147.30750 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 49.10250 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 147.30750 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 49.10250 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 147.30750 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 49.10250 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 49.10250 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 49.10250 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 147.30750 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 49.10250 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 147.30750 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 147.30750 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 147.30750 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 49.10250 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 49.10250 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 147.30750 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 147.30750 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 49.10250 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 49.10250 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 49.10250 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 49.10250 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 147.30750 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 49.10250 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 147.30750 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 49.10250 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 147.30750 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 147.30750 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 147.30750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 G B 1 P G B 1 OP3 -0.084 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 GLU A 3 -129.69 -68.66 REMARK 500 LYS A 4 -45.74 -160.53 REMARK 500 PHE A 5 98.38 57.34 REMARK 500 THR A 8 135.08 175.64 REMARK 500 LYS A 9 155.67 65.24 REMARK 500 ASP A 21 3.93 34.07 REMARK 500 LYS A 24 -91.78 4.37 REMARK 500 ALA A 30 -74.38 -40.92 REMARK 500 VAL A 34 -72.26 -59.12 REMARK 500 ALA A 36 23.45 -71.65 REMARK 500 LYS A 37 -56.53 -155.20 REMARK 500 THR A 38 7.33 -63.02 REMARK 500 TYR A 39 7.63 -170.83 REMARK 500 ALA A 42 106.94 177.33 REMARK 500 ASP A 47 -33.26 -35.12 REMARK 500 ASP A 50 54.97 -93.78 REMARK 500 ILE A 60 0.14 -153.56 REMARK 500 THR A 61 109.05 61.55 REMARK 500 THR A 71 -167.93 -105.01 REMARK 500 VAL A 127 113.76 15.67 REMARK 500 ASP A 142 69.29 -174.18 REMARK 500 GLU A 143 -16.21 -32.93 REMARK 500 GLU A 155 -35.66 -38.02 REMARK 500 LEU A 156 -71.67 -65.94 REMARK 500 LEU A 157 -71.17 -33.78 REMARK 500 SER A 158 -1.27 -51.31 REMARK 500 ASP A 161 60.41 87.33 REMARK 500 ASP A 166 -9.08 -56.43 REMARK 500 ALA A 177 -74.66 -47.56 REMARK 500 LEU A 178 -36.43 -31.68 REMARK 500 ASP A 181 103.39 -40.41 REMARK 500 ALA A 192 -7.80 -54.29 REMARK 500 ILE A 199 -92.62 -7.10 REMARK 500 GLU A 201 124.89 23.62 REMARK 500 ALA A 205 -75.86 -53.38 REMARK 500 ILE A 206 -40.80 52.85 REMARK 500 ASP A 207 25.36 -75.22 REMARK 500 LEU A 211 128.35 -174.50 REMARK 500 ASP A 216 144.08 -172.93 REMARK 500 ARG A 223 -93.40 -89.87 REMARK 500 ILE A 247 -60.61 68.75 REMARK 500 THR A 256 18.46 -149.91 REMARK 500 PHE A 261 73.58 65.43 REMARK 500 ARG A 262 13.41 47.34 REMARK 500 LEU A 264 150.50 -35.85 REMARK 500 ALA A 270 137.42 -33.52 REMARK 500 LEU A 278 100.47 39.70 REMARK 500 GLU A 285 -3.52 -152.03 REMARK 500 ASP A 314 -1.09 -55.55 REMARK 500 ARG A 333 -112.55 58.52 REMARK 500 REMARK 500 THIS ENTRY HAS 51 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 U B 8 0.07 SIDE CHAIN REMARK 500 G B 22 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1398 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 25 OG1 REMARK 620 2 THR A 61 OG1 74.8 REMARK 620 3 GNP A1397 O1G 107.7 100.1 REMARK 620 4 GNP A1397 O2B 77.3 150.3 79.1 REMARK 620 5 GNP A1397 O2A 98.5 125.3 132.4 68.6 REMARK 620 6 GNP A1397 O3G 164.9 103.8 57.4 100.6 94.5 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D8T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ELONGATION FACTOR, TU ( EF-TU-MGGDP) COMPLEXED REMARK 900 WITH GE2270A, A THIAZOLYL PEPTIDE ANTIBIOTIC REMARK 900 RELATED ID: 1DG1 RELATED DB: PDB REMARK 900 WHOLE, UNMODIFIED, EF-TU(ELONGATION FACTOR TU). REMARK 900 RELATED ID: 1EFC RELATED DB: PDB REMARK 900 INTACT ELONGATION FACTOR FROM E.COLI REMARK 900 RELATED ID: 1EFM RELATED DB: PDB REMARK 900 TRYPSIN-MODIFIED ELONGATION FACTOR TU (EF-TU -GDP) REMARK 900 RELATED ID: 1EFU RELATED DB: PDB REMARK 900 ELONGATION FACTOR COMPLEX EF-TU/EF-TS FROM ESCHERICHIA COLI REMARK 900 RELATED ID: 1ETU RELATED DB: PDB REMARK 900 ELONGATION FACTOR TU (DOMAIN I) - GUANOSINE DIPHOSPHATE COMPLEX REMARK 900 RELATED ID: 1LS2 RELATED DB: PDB REMARK 900 FITTING OF EF-TU AND TRNA IN THE LOW RESOLUTION CRYO-EM MAPOF AN EF- REMARK 900 TU TERNARY COMPLEX (GDP AND KIRROMYCIN) BOUND TOE. COLI 70S RIBOSOME REMARK 900 RELATED ID: 1QZD RELATED DB: PDB REMARK 900 EF-TU.KIRROMYCIN COORDINATES FITTED INTO THE CRYO-EM MAP OFEF-TU REMARK 900 TERNARY COMPLEX (GDP .KIRROMYCIN) BOUND 70S RIBOSOME DBREF 1OB2 A 1 393 UNP P0CE48 EFTU2_ECOLI 2 39 DBREF 1OB2 B 1 77 PDB 1OB2 1OB2 1 77 SEQADV 1OB2 ALA A 1 UNP P0CE48 SER 2 CONFLICT SEQRES 1 A 393 ALA LYS GLU LYS PHE GLU ARG THR LYS PRO HIS VAL ASN SEQRES 2 A 393 VAL GLY THR ILE GLY HIS VAL ASP HIS GLY LYS THR THR SEQRES 3 A 393 LEU THR ALA ALA ILE THR THR VAL LEU ALA LYS THR TYR SEQRES 4 A 393 GLY GLY ALA ALA ARG ALA PHE ASP GLN ILE ASP ASN ALA SEQRES 5 A 393 PRO GLU GLU LYS ALA ARG GLY ILE THR ILE ASN THR SER SEQRES 6 A 393 HIS VAL GLU TYR ASP THR PRO THR ARG HIS TYR ALA HIS SEQRES 7 A 393 VAL ASP CYS PRO GLY HIS ALA ASP TYR VAL LYS ASN MET SEQRES 8 A 393 ILE THR GLY ALA ALA GLN MET ASP GLY ALA ILE LEU VAL SEQRES 9 A 393 VAL ALA ALA THR ASP GLY PRO MET PRO GLN THR ARG GLU SEQRES 10 A 393 HIS ILE LEU LEU GLY ARG GLN VAL GLY VAL PRO TYR ILE SEQRES 11 A 393 ILE VAL PHE LEU ASN LYS CYS ASP MET VAL ASP ASP GLU SEQRES 12 A 393 GLU LEU LEU GLU LEU VAL GLU MET GLU VAL ARG GLU LEU SEQRES 13 A 393 LEU SER GLN TYR ASP PHE PRO GLY ASP ASP THR PRO ILE SEQRES 14 A 393 VAL ARG GLY SER ALA LEU LYS ALA LEU GLU GLY ASP ALA SEQRES 15 A 393 GLU TRP GLU ALA LYS ILE LEU GLU LEU ALA GLY PHE LEU SEQRES 16 A 393 ASP SER TYR ILE PRO GLU PRO GLU ARG ALA ILE ASP LYS SEQRES 17 A 393 PRO PHE LEU LEU PRO ILE GLU ASP VAL PHE SER ILE SER SEQRES 18 A 393 GLY ARG GLY THR VAL VAL THR GLY ARG VAL GLU ARG GLY SEQRES 19 A 393 ILE ILE LYS VAL GLY GLU GLU VAL GLU ILE VAL GLY ILE SEQRES 20 A 393 LYS GLU THR GLN LYS SER THR CYS THR GLY VAL GLU MET SEQRES 21 A 393 PHE ARG LYS LEU LEU ASP GLU GLY ARG ALA GLY GLU ASN SEQRES 22 A 393 VAL GLY VAL LEU LEU ARG GLY ILE LYS ARG GLU GLU ILE SEQRES 23 A 393 GLU ARG GLY GLN VAL LEU ALA LYS PRO GLY THR ILE LYS SEQRES 24 A 393 PRO HIS THR LYS PHE GLU SER GLU VAL TYR ILE LEU SER SEQRES 25 A 393 LYS ASP GLU GLY GLY ARG HIS THR PRO PHE PHE LYS GLY SEQRES 26 A 393 TYR ARG PRO GLN PHE TYR PHE ARG THR THR ASP VAL THR SEQRES 27 A 393 GLY THR ILE GLU LEU PRO GLU GLY VAL GLU MET VAL MET SEQRES 28 A 393 PRO GLY ASP ASN ILE LYS MET VAL VAL THR LEU ILE HIS SEQRES 29 A 393 PRO ILE ALA MET ASP ASP GLY LEU ARG PHE ALA ILE ARG SEQRES 30 A 393 GLU GLY GLY ARG THR VAL GLY ALA GLY VAL VAL ALA LYS SEQRES 31 A 393 VAL LEU SER SEQRES 1 B 77 G C G G A U U U A 2MG C U C SEQRES 2 B 77 A G H2U H2U G G G A G A G C M2G SEQRES 3 B 77 C C A G A OMC U OMG A A YG A PSU SEQRES 4 B 77 5MC U G G A G 7MG U C 5MC U G U SEQRES 5 B 77 G U PSU C G 1MA U C C A C A G SEQRES 6 B 77 A A U U C G C A C C A PHA MODRES 1OB2 2MG B 10 G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1OB2 H2U B 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1OB2 H2U B 17 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1OB2 M2G B 26 G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1OB2 OMC B 32 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 1OB2 OMG B 34 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1OB2 YG B 37 G WYBUTOSINE MODRES 1OB2 PSU B 39 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1OB2 5MC B 40 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1OB2 7MG B 46 G MODRES 1OB2 5MC B 49 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1OB2 PSU B 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1OB2 1MA B 58 A MODRES 1OB2 PHA B 77 PHE PHENYLALANINAL HET 2MG B 10 24 HET H2U B 16 20 HET H2U B 17 20 HET M2G B 26 25 HET OMC B 32 21 HET OMG B 34 24 HET YG B 37 39 HET PSU B 39 20 HET 5MC B 40 21 HET 7MG B 46 24 HET 5MC B 49 21 HET PSU B 55 20 HET 1MA B 58 23 HET PHA B 77 11 HET GLC C 1 11 HET FRU C 2 12 HET KIR A1394 57 HET GNP A1397 32 HET MG A1398 1 HETNAM 2MG 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE HETNAM M2G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM YG WYBUTOSINE HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE HETNAM 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE HETNAM 1MA 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM PHA PHENYLALANINAL HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM FRU BETA-D-FRUCTOFURANOSE HETNAM KIR KIRROMYCIN HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETSYN YG Y-BASE; 1H-IMIDAZO(1,2-ALPHA)PURINE-7-BUTANOIC ACID,4, HETSYN 2 YG 9-DIHYDRO-ALPHA-((METHOXYCARBONYL)AMINO)-4,6-DIMETHYL- HETSYN 3 YG 9-OXO-METHYL ESTER HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN FRU BETA-D-FRUCTOSE; D-FRUCTOSE; FRUCTOSE HETSYN KIR MOCIMYCIN; DELVOMYCIN; MYC-8003 FORMUL 2 2MG C11 H16 N5 O8 P FORMUL 2 H2U 2(C9 H15 N2 O9 P) FORMUL 2 M2G C12 H18 N5 O8 P FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 2 OMG C11 H16 N5 O8 P FORMUL 2 YG C21 H29 N6 O12 P FORMUL 2 PSU 2(C9 H13 N2 O9 P) FORMUL 2 5MC 2(C10 H16 N3 O8 P) FORMUL 2 7MG C11 H18 N5 O8 P FORMUL 2 1MA C11 H16 N5 O7 P FORMUL 2 PHA C9 H11 N O FORMUL 3 GLC C6 H12 O6 FORMUL 3 FRU C6 H12 O6 FORMUL 4 KIR C43 H60 N2 O12 FORMUL 5 GNP C10 H17 N6 O13 P3 FORMUL 6 MG MG 2+ HELIX 1 1 GLY A 23 TYR A 39 1 17 HELIX 2 2 ALA A 45 ASP A 50 1 6 HELIX 3 3 ALA A 52 GLY A 59 1 8 HELIX 4 4 HIS A 84 ASP A 86 5 3 HELIX 5 5 TYR A 87 GLN A 97 1 11 HELIX 6 6 MET A 112 VAL A 125 1 14 HELIX 7 7 LYS A 136 VAL A 140 5 5 HELIX 8 8 ASP A 142 ASP A 161 1 20 HELIX 9 9 SER A 173 GLY A 180 1 8 HELIX 10 10 ASP A 181 GLY A 193 1 13 HELIX 11 11 GLY A 193 TYR A 198 1 6 HELIX 12 12 LYS A 282 ILE A 286 5 5 HELIX 13 13 SER A 312 GLY A 316 5 5 SHEET 1 AA 6 SER A 65 ASP A 70 0 SHEET 2 AA 6 HIS A 75 ASP A 80 -1 O TYR A 76 N TYR A 69 SHEET 3 AA 6 HIS A 11 ILE A 17 1 O VAL A 12 N ALA A 77 SHEET 4 AA 6 ALA A 101 ALA A 106 1 O ILE A 102 N ILE A 17 SHEET 5 AA 6 ILE A 130 ASN A 135 1 O ILE A 131 N LEU A 103 SHEET 6 AA 6 ILE A 169 ARG A 171 1 O VAL A 170 N LEU A 134 SHEET 1 AB 4 LEU A 211 PRO A 213 0 SHEET 2 AB 4 VAL A 291 ALA A 293 -1 O LEU A 292 N LEU A 212 SHEET 3 AB 4 GLU A 241 VAL A 245 -1 O GLU A 243 N ALA A 293 SHEET 4 AB 4 GLN A 251 THR A 254 -1 O GLN A 251 N ILE A 244 SHEET 1 AC 3 ASP A 216 SER A 219 0 SHEET 2 AC 3 THR A 225 ARG A 230 -1 O VAL A 226 N PHE A 218 SHEET 3 AC 3 ASN A 273 VAL A 276 -1 O VAL A 274 N GLY A 229 SHEET 1 AD 7 PRO A 300 TYR A 309 0 SHEET 2 AD 7 ASN A 355 ALA A 367 -1 O ILE A 356 N VAL A 308 SHEET 3 AD 7 THR A 335 THR A 340 -1 O THR A 338 N ILE A 363 SHEET 4 AD 7 GLN A 329 PHE A 332 -1 O PHE A 330 N VAL A 337 SHEET 5 AD 7 ARG A 373 GLU A 378 -1 O ALA A 375 N TYR A 331 SHEET 6 AD 7 ARG A 381 VAL A 391 -1 O ARG A 381 N GLU A 378 SHEET 7 AD 7 PRO A 300 TYR A 309 -1 O GLU A 305 N LYS A 390 LINK O3' A B 9 P 2MG B 10 1555 1555 1.60 LINK O3' 2MG B 10 P C B 11 1555 1555 1.61 LINK O3' G B 15 P H2U B 16 1555 1555 1.61 LINK O3' H2U B 16 P H2U B 17 1555 1555 1.61 LINK O3' H2U B 17 P G B 18 1555 1555 1.61 LINK O3' C B 25 P M2G B 26 1555 1555 1.61 LINK O3' M2G B 26 P C B 27 1555 1555 1.61 LINK O3' A B 31 P OMC B 32 1555 1555 1.61 LINK O3' OMC B 32 P U B 33 1555 1555 1.61 LINK O3' U B 33 P OMG B 34 1555 1555 1.61 LINK O3' OMG B 34 P A B 35 1555 1555 1.61 LINK O3' A B 36 P YG B 37 1555 1555 1.61 LINK O3' YG B 37 P A B 38 1555 1555 1.61 LINK O3' A B 38 P PSU B 39 1555 1555 1.61 LINK O3' PSU B 39 P 5MC B 40 1555 1555 1.61 LINK O3' 5MC B 40 P U B 41 1555 1555 1.61 LINK O3' G B 45 P 7MG B 46 1555 1555 1.61 LINK O3' 7MG B 46 P U B 47 1555 1555 1.61 LINK O3' C B 48 P 5MC B 49 1555 1555 1.60 LINK O3' 5MC B 49 P U B 50 1555 1555 1.61 LINK O3' U B 54 P PSU B 55 1555 1555 1.60 LINK O3' PSU B 55 P C B 56 1555 1555 1.61 LINK O3' G B 57 P 1MA B 58 1555 1555 1.60 LINK O3' 1MA B 58 P U B 59 1555 1555 1.60 LINK O3' A B 76 C PHA B 77 1555 1555 1.31 LINK C1 GLC C 1 O2 FRU C 2 1555 1555 1.45 LINK OG1 THR A 25 MG MG A1398 1555 1555 2.03 LINK OG1 THR A 61 MG MG A1398 1555 1555 2.53 LINK O1G GNP A1397 MG MG A1398 1555 1555 1.86 LINK O2B GNP A1397 MG MG A1398 1555 1555 2.34 LINK O2A GNP A1397 MG MG A1398 1555 1555 2.84 LINK O3G GNP A1397 MG MG A1398 1555 1555 2.83 CISPEP 1 ILE A 199 PRO A 200 0 0.25 CRYST1 196.410 196.410 196.410 90.00 90.00 90.00 P 41 3 2 24 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 0.005091 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005091 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005091 0.00000