HEADER GENE REGULATION/RNA 04-DEC-98 1B23 TITLE E. COLI CYSTEINYL-TRNA AND T. AQUATICUS ELONGATION FACTOR EF-TU:GTP TITLE 2 TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINYL TRNA; COMPND 3 CHAIN: R; COMPND 4 SYNONYM: CYS-TRNA; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: AMINOACYL LINK BETWEEN A76 AND CYS77; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ELONGATION FACTOR TU; COMPND 9 CHAIN: P; COMPND 10 SYNONYM: EF-TU; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 6 ORGANISM_TAXID: 271; SOURCE 7 STRAIN: YT-1; SOURCE 8 GENE: TUFA; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSLATION ELONGATION FACTOR, TRANSFER RNA, PROTEIN SYNTHESIS, GENE KEYWDS 2 REGULATION-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.NISSEN,M.KJELDGAARD,S.THIRUP,J.NYBORG REVDAT 7 09-AUG-23 1B23 1 REMARK LINK REVDAT 6 03-JUL-19 1B23 1 COMPND REMARK FORMUL LINK REVDAT 5 16-NOV-11 1B23 1 VERSN HETATM REVDAT 4 24-FEB-09 1B23 1 VERSN REVDAT 3 01-APR-03 1B23 1 JRNL REVDAT 2 22-DEC-99 1B23 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 07-DEC-98 1B23 0 JRNL AUTH P.NISSEN,S.THIRUP,M.KJELDGAARD,J.NYBORG JRNL TITL THE CRYSTAL STRUCTURE OF CYS-TRNACYS-EF-TU-GDPNP REVEALS JRNL TITL 2 GENERAL AND SPECIFIC FEATURES IN THE TERNARY COMPLEX AND IN JRNL TITL 3 TRNA. JRNL REF STRUCTURE FOLD.DES. V. 7 143 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10368282 JRNL DOI 10.1016/S0969-2126(99)80021-5 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.NISSEN,M.KJELDGAARD,S.THIRUP,G.POLEKHINA,L.RESHETNIKOVA, REMARK 1 AUTH 2 B.F.C.CLARK,J.NYBORG REMARK 1 TITL CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF PHE-TRNAPHE, REMARK 1 TITL 2 EF-TU, AND A GTP ANALOG REMARK 1 REF SCIENCE V. 270 1464 1995 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 18043 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) : 0.206 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1424 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1314 REMARK 3 BIN R VALUE (WORKING SET) : 0.3620 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 107 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3144 REMARK 3 NUCLEIC ACID ATOMS : 1584 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 261 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -31.50000 REMARK 3 B22 (A**2) : -4.00000 REMARK 3 B33 (A**2) : 14.90000 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) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.46 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) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.56 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.880 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 5.410 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 1.500 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.500 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.500 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.300 ; 5.000 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : TRNA-MULTI-ENDO.PARAM REMARK 3 PARAMETER FILE 3 : GTP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TRNA-MULTI-ENDO.TOP REMARK 3 TOPOLOGY FILE 3 : GTP.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ANISOTROPIC SCALING WAS CRUCIAL FOR REFINEMENT. ANISOTROPIC REMARK 3 SCALEFACTORS DERIVED FROM 4.0 - 2.6 A AMPLITUDES REMARK 3 REMARK 3 THE ISOPENTENYL GROUP OF MIA R 37 AND THE N-TERMINAL ALA P REMARK 3 1 RESIDUE WERE STEREOCHEMICALLY MODELED REMARK 4 REMARK 4 1B23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000000207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.098 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18435 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39600 REMARK 200 FOR SHELL : 2.400 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: ANISOTROPIC DIFFRACTION REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1 M (NH4)2SO4, 30 MM TRIS, 5 MM MES, REMARK 280 10 MM MGCL2, 10 MM DTT, 1 MM GDPNP PH 6.7, 4 DEG. C, HANGING REMARK 280 DROP, VAPOR DIFFUSION - HANGING DROP, TEMPERATURE 277K, VAPOR REMARK 280 DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 66.49000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 77.44000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 66.49000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 77.44000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.49000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 77.44000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 66.49000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 77.44000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 63.37500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 77.44000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 63.37500 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 77.44000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 63.37500 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 77.44000 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 63.37500 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 77.44000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 63.37500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 66.49000 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 63.37500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 66.49000 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 63.37500 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 66.49000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 63.37500 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 66.49000 REMARK 290 SMTRY3 16 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: R, P 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG R 179 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MIA R 37 C12 C13 C14 C15 C16 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 N4 C R 72 O4 U R 73 1.57 REMARK 500 N4 C R 75 OG1 THR P 232 1.70 REMARK 500 N4 C R 72 C4 U R 73 1.77 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 G R 1 P G R 1 OP3 -0.085 REMARK 500 U R 7 C1' U R 7 N1 -0.238 REMARK 500 A R 22 N9 A R 22 C4 -0.065 REMARK 500 C R 72 C1' C R 72 N1 0.200 REMARK 500 C R 75 O5' C R 75 C5' 0.256 REMARK 500 C R 75 C1' C R 75 N1 0.360 REMARK 500 ALA P 1 C LYS P 2 N -0.173 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 U R 7 N1 - C1' - C2' ANGL. DEV. = 23.4 DEGREES REMARK 500 U R 7 C6 - N1 - C1' ANGL. DEV. = -22.9 DEGREES REMARK 500 U R 7 C2 - N1 - C1' ANGL. DEV. = 22.3 DEGREES REMARK 500 A R 22 C8 - N9 - C4 ANGL. DEV. = 2.7 DEGREES REMARK 500 C R 72 N1 - C1' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 C R 75 O5' - C5' - C4' ANGL. DEV. = -43.9 DEGREES REMARK 500 C R 75 P - O5' - C5' ANGL. DEV. = -31.6 DEGREES REMARK 500 C R 75 C4' - C3' - O3' ANGL. DEV. = 38.1 DEGREES REMARK 500 C R 75 C2' - C3' - O3' ANGL. DEV. = -22.6 DEGREES REMARK 500 C R 75 O4' - C1' - N1 ANGL. DEV. = 19.7 DEGREES REMARK 500 C R 75 C2 - N1 - C1' ANGL. DEV. = 7.1 DEGREES REMARK 500 C R 75 C3' - O3' - P ANGL. DEV. = 11.7 DEGREES REMARK 500 LYS P 2 C - N - CA ANGL. DEV. = 38.9 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 LYS P 2 -60.00 140.11 REMARK 500 ILE P 50 -70.99 -83.03 REMARK 500 THR P 72 -162.35 -100.06 REMARK 500 ASP P 216 45.80 -85.86 REMARK 500 LEU P 222 119.43 -165.12 REMARK 500 ALA P 259 141.93 177.35 REMARK 500 HIS P 273 70.06 55.87 REMARK 500 ARG P 274 10.92 56.37 REMARK 500 GLN P 302 -168.56 -75.44 REMARK 500 THR P 314 -41.37 -131.24 REMARK 500 PHE P 316 150.09 177.67 REMARK 500 ARG P 339 78.11 -117.40 REMARK 500 ARG P 345 -117.68 54.24 REMARK 500 ALA P 379 109.84 -54.51 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 P 1 LYS P 2 96.61 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 C R 72 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 R 77 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A R 76 O5' REMARK 620 2 A R 76 OP2 52.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG P 407 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR P 25 OG1 REMARK 620 2 THR P 62 OG1 80.9 REMARK 620 3 GNP P 406 O2B 80.4 145.4 REMARK 620 4 GNP P 406 N3B 120.1 116.2 52.5 REMARK 620 5 GNP P 406 O3G 162.3 88.0 101.9 53.4 REMARK 620 6 HOH P 410 O 88.2 109.4 98.8 128.7 108.6 REMARK 620 7 HOH P 419 O 74.6 69.3 77.8 62.4 88.6 162.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG P 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 P 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 P 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 77 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 179 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CYS R 976 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP P 406 DBREF 1B23 P 1 405 UNP Q01698 EFTU_THEAQ 1 405 DBREF 1B23 R 1 76 PDB 1B23 1B23 1 76 SEQRES 1 R 74 G G C G C G U 4SU A A C A A SEQRES 2 R 74 A G C G G H2U H2U A U G U A G SEQRES 3 R 74 C G G A PSU U G C A MIA A PSU C SEQRES 4 R 74 C G U C U A G U C C G G 5MU SEQRES 5 R 74 PSU C G A C U C C G G A A C SEQRES 6 R 74 G C G C C U C C A SEQRES 1 P 405 ALA LYS GLY GLU PHE ILE ARG THR LYS PRO HIS VAL ASN SEQRES 2 P 405 VAL GLY THR ILE GLY HIS VAL ASP HIS GLY LYS THR THR SEQRES 3 P 405 LEU THR ALA ALA LEU THR TYR VAL ALA ALA ALA GLU ASN SEQRES 4 P 405 PRO ASN VAL GLU VAL LYS ASP TYR GLY ASP ILE ASP LYS SEQRES 5 P 405 ALA PRO GLU GLU ARG ALA ARG GLY ILE THR ILE ASN THR SEQRES 6 P 405 ALA HIS VAL GLU TYR GLU THR ALA LYS ARG HIS TYR SER SEQRES 7 P 405 HIS VAL ASP CYS PRO GLY HIS ALA ASP TYR ILE LYS ASN SEQRES 8 P 405 MET ILE THR GLY ALA ALA GLN MET ASP GLY ALA ILE LEU SEQRES 9 P 405 VAL VAL SER ALA ALA ASP GLY PRO MET PRO GLN THR ARG SEQRES 10 P 405 GLU HIS ILE LEU LEU ALA ARG GLN VAL GLY VAL PRO TYR SEQRES 11 P 405 ILE VAL VAL PHE MET ASN LYS VAL ASP MET VAL ASP ASP SEQRES 12 P 405 PRO GLU LEU LEU ASP LEU VAL GLU MET GLU VAL ARG ASP SEQRES 13 P 405 LEU LEU ASN GLN TYR GLU PHE PRO GLY ASP GLU VAL PRO SEQRES 14 P 405 VAL ILE ARG GLY SER ALA LEU LEU ALA LEU GLU GLU MET SEQRES 15 P 405 HIS LYS ASN PRO LYS THR LYS ARG GLY GLU ASN GLU TRP SEQRES 16 P 405 VAL ASP LYS ILE TRP GLU LEU LEU ASP ALA ILE ASP GLU SEQRES 17 P 405 TYR ILE PRO THR PRO VAL ARG ASP VAL ASP LYS PRO PHE SEQRES 18 P 405 LEU MET PRO VAL GLU ASP VAL PHE THR ILE THR GLY ARG SEQRES 19 P 405 GLY THR VAL ALA THR GLY ARG ILE GLU ARG GLY LYS VAL SEQRES 20 P 405 LYS VAL GLY ASP GLU VAL GLU ILE VAL GLY LEU ALA PRO SEQRES 21 P 405 GLU THR ARG LYS THR VAL VAL THR GLY VAL GLU MET HIS SEQRES 22 P 405 ARG LYS THR LEU GLN GLU GLY ILE ALA GLY ASP ASN VAL SEQRES 23 P 405 GLY LEU LEU LEU ARG GLY VAL SER ARG GLU GLU VAL GLU SEQRES 24 P 405 ARG GLY GLN VAL LEU ALA LYS PRO GLY SER ILE THR PRO SEQRES 25 P 405 HIS THR LYS PHE GLU ALA SER VAL TYR ILE LEU LYS LYS SEQRES 26 P 405 GLU GLU GLY GLY ARG HIS THR GLY PHE PHE THR GLY TYR SEQRES 27 P 405 ARG PRO GLN PHE TYR PHE ARG THR THR ASP VAL THR GLY SEQRES 28 P 405 VAL VAL ARG LEU PRO GLN GLY VAL GLU MET VAL MET PRO SEQRES 29 P 405 GLY ASP ASN VAL THR PHE THR VAL GLU LEU ILE LYS PRO SEQRES 30 P 405 VAL ALA LEU GLU GLU GLY LEU ARG PHE ALA ILE ARG GLU SEQRES 31 P 405 GLY GLY ARG THR VAL GLY ALA GLY VAL VAL THR LYS ILE SEQRES 32 P 405 LEU GLU MODRES 1B23 4SU R 8 U 4-THIOURIDINE-5'-MONOPHOSPHATE MODRES 1B23 H2U R 20 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1B23 H2U R 21 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1B23 PSU R 32 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1B23 MIA R 37 A MODRES 1B23 PSU R 39 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1B23 5MU R 54 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 1B23 PSU R 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE HET 4SU R 8 20 HET H2U R 20 20 HET H2U R 21 20 HET PSU R 32 20 HET MIA R 37 29 HET PSU R 39 20 HET 5MU R 54 21 HET PSU R 55 20 HET MG R 77 1 HET MG R 179 1 HET CYS R 976 6 HET MG P 407 1 HET SO4 P 408 5 HET SO4 P 409 5 HET GNP P 406 32 HETNAM 4SU 4-THIOURIDINE-5'-MONOPHOSPHATE HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM MIA 2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CYS CYSTEINE HETNAM SO4 SULFATE ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 1 4SU C9 H13 N2 O8 P S FORMUL 1 H2U 2(C9 H15 N2 O9 P) FORMUL 1 PSU 3(C9 H13 N2 O9 P) FORMUL 1 MIA C16 H24 N5 O7 P S FORMUL 1 5MU C10 H15 N2 O9 P FORMUL 3 MG 3(MG 2+) FORMUL 5 CYS C3 H7 N O2 S FORMUL 7 SO4 2(O4 S 2-) FORMUL 9 GNP C10 H17 N6 O13 P3 FORMUL 10 HOH *261(H2 O) HELIX 1 1 LYS P 24 GLU P 38 1 15 HELIX 2 2 TYR P 47 ILE P 50 1 4 HELIX 3 3 PRO P 54 ARG P 59 1 6 HELIX 4 4 ALA P 86 GLN P 98 5 13 HELIX 5 5 PRO P 114 VAL P 126 1 13 HELIX 6 6 VAL P 138 MET P 140 5 3 HELIX 7 7 PRO P 144 TYR P 161 1 18 HELIX 8 8 ALA P 175 LYS P 184 1 10 HELIX 9 9 GLU P 194 TYR P 209 1 16 HELIX 10 10 LYS P 325 GLU P 327 5 3 SHEET 1 A 6 VAL P 170 ARG P 172 0 SHEET 2 A 6 TYR P 130 ASN P 136 1 N VAL P 133 O ILE P 171 SHEET 3 A 6 GLY P 101 SER P 107 1 N ALA P 102 O TYR P 130 SHEET 4 A 6 PRO P 10 ILE P 17 1 N GLY P 15 O GLY P 101 SHEET 5 A 6 ARG P 75 ASP P 81 1 N HIS P 76 O PRO P 10 SHEET 6 A 6 ALA P 66 GLU P 71 -1 N TYR P 70 O TYR P 77 SHEET 1 B 4 LEU P 222 PRO P 224 0 SHEET 2 B 4 VAL P 303 LYS P 306 -1 N LEU P 304 O MET P 223 SHEET 3 B 4 GLU P 252 VAL P 256 -1 N VAL P 256 O VAL P 303 SHEET 4 B 4 LYS P 264 VAL P 266 -1 N THR P 265 O VAL P 253 SHEET 1 C 4 ASP P 227 ILE P 231 0 SHEET 2 C 4 GLY P 235 ARG P 241 -1 N THR P 239 O ASP P 227 SHEET 3 C 4 ASN P 285 LEU P 290 -1 N LEU P 290 O THR P 236 SHEET 4 C 4 VAL P 267 VAL P 270 -1 N GLY P 269 O LEU P 289 SHEET 1 D 2 LYS P 246 LYS P 248 0 SHEET 2 D 2 GLU P 279 ILE P 281 -1 N GLY P 280 O VAL P 247 SHEET 1 E 7 GLY P 351 ARG P 354 0 SHEET 2 E 7 ASN P 367 LEU P 374 -1 N GLU P 373 O VAL P 352 SHEET 3 E 7 LYS P 315 ILE P 322 -1 N VAL P 320 O VAL P 368 SHEET 4 E 7 ARG P 393 LYS P 402 -1 N LYS P 402 O GLU P 317 SHEET 5 E 7 ARG P 385 GLU P 390 -1 N GLU P 390 O ARG P 393 SHEET 6 E 7 GLN P 341 PHE P 344 -1 N TYR P 343 O ALA P 387 SHEET 7 E 7 THR P 347 THR P 350 -1 N VAL P 349 O PHE P 342 LINK O3' U R 7 P 4SU R 8 1555 1555 1.61 LINK O3' 4SU R 8 P A R 9 1555 1555 1.61 LINK O3' G R 19 P H2U R 20 1555 1555 1.60 LINK O3' H2U R 20 P H2U R 21 1555 1555 1.61 LINK O3' H2U R 21 P A R 22 1555 1555 1.60 LINK O3' A R 31 P PSU R 32 1555 1555 1.60 LINK O3' PSU R 32 P U R 33 1555 1555 1.61 LINK O3' A R 36 P MIA R 37 1555 1555 1.61 LINK O3' MIA R 37 P A R 38 1555 1555 1.61 LINK O3' A R 38 P PSU R 39 1555 1555 1.62 LINK O3' PSU R 39 P C R 40 1555 1555 1.61 LINK O3' G R 53 P 5MU R 54 1555 1555 1.60 LINK O3' 5MU R 54 P PSU R 55 1555 1555 1.61 LINK O3' PSU R 55 P C R 56 1555 1555 1.61 LINK O3' A R 76 C CYS R 976 1555 1555 1.31 LINK O5' A R 76 MG MG R 77 1555 1555 3.08 LINK OP2 A R 76 MG MG R 77 1555 1555 1.63 LINK OG1 THR P 25 MG MG P 407 1555 1555 2.13 LINK OG1 THR P 62 MG MG P 407 1555 1555 2.25 LINK O2B GNP P 406 MG MG P 407 1555 1555 1.96 LINK N3B GNP P 406 MG MG P 407 1555 1555 3.15 LINK O3G GNP P 406 MG MG P 407 1555 1555 2.08 LINK MG MG P 407 O HOH P 410 1555 1555 1.94 LINK MG MG P 407 O HOH P 419 1555 1555 2.60 SITE 1 AC1 5 THR P 25 THR P 62 GNP P 406 HOH P 410 SITE 2 AC1 5 HOH P 419 SITE 1 AC2 6 ARG P 339 VAL P 352 ARG P 354 HOH P 442 SITE 2 AC2 6 HOH P 463 HOH P 548 SITE 1 AC3 4 MET P 113 PRO P 114 ARG P 117 HOH P 423 SITE 1 AC4 2 C R 75 A R 76 SITE 1 AC5 1 G R 70 SITE 1 AC6 6 HIS P 67 HIS P 273 ARG P 274 ASN P 285 SITE 2 AC6 6 VAL P 286 A R 76 SITE 1 AC7 22 VAL P 20 ASP P 21 HIS P 22 GLY P 23 SITE 2 AC7 22 LYS P 24 THR P 25 THR P 26 TYR P 47 SITE 3 AC7 22 ILE P 61 THR P 62 GLY P 84 ASN P 136 SITE 4 AC7 22 LYS P 137 ASP P 139 MET P 140 SER P 174 SITE 5 AC7 22 ALA P 175 LEU P 176 MG P 407 HOH P 410 SITE 6 AC7 22 HOH P 419 HOH P 524 CRYST1 126.750 132.980 154.880 90.00 90.00 90.00 F 2 2 2 16 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 0.007889 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006457 0.00000