HEADER TRANSFERASE/RNA 17-FEB-06 2DEU
TITLE COCRYSTAL STRUCTURE OF AN RNA SULFURATION ENZYME MNMA AND TRNA-GLU IN
TITLE 2 THE ADENYLATED INTERMEDIATE STATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRNA;
COMPND 3 CHAIN: C, D;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: TRNA-SPECIFIC 2-THIOURIDYLASE MNMA;
COMPND 7 CHAIN: A, B;
COMPND 8 SYNONYM: RNA SULFURATION ENZYME MNMA;
COMPND 9 EC: 2.8.1.-;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION.;
SOURCE 4 MOL_ID: 2;
SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 6 ORGANISM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: B834(DE3);
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PQE80L
KEYWDS PROTEIN-RNA COMPLEX, ADENYLATED INTERMEDIATE OF RNA, TRANSFERASE-RNA
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR T.NUMATA,Y.IKEUCHI,S.FUKAI,T.SUZUKI,O.NUREKI
REVDAT 3 25-OCT-23 2DEU 1 REMARK SEQADV LINK
REVDAT 2 13-JAN-09 2DEU 1 COMPND VERSN
REVDAT 1 15-AUG-06 2DEU 0
JRNL AUTH T.NUMATA,Y.IKEUCHI,S.FUKAI,T.SUZUKI,O.NUREKI
JRNL TITL SNAPSHOTS OF TRNA SULPHURATION VIA AN ADENYLATED
JRNL TITL 2 INTERMEDIATE
JRNL REF NATURE V. 442 419 2006
JRNL REFN ISSN 0028-0836
JRNL PMID 16871210
JRNL DOI 10.1038/NATURE04896
REMARK 2
REMARK 2 RESOLUTION. 3.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
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 : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.16
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.6
REMARK 3 NUMBER OF REFLECTIONS : 28987
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) : 0.281
REMARK 3 FREE R VALUE : 0.318
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 1456
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 : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.40
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.60
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.70
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.3580
REMARK 3 BIN FREE R VALUE : 0.3980
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 226
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5708
REMARK 3 NUCLEIC ACID ATOMS : 3146
REMARK 3 HETEROGEN ATOMS : 54
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.45
REMARK 3 ESD FROM SIGMAA (A) : 0.89
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) : 0.57
REMARK 3 ESD FROM C-V SIGMAA (A) : 1.05
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.008
REMARK 3 BOND ANGLES (DEGREES) : 1.400
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.60
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.350
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2DEU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-FEB-06.
REMARK 100 THE DEPOSITION ID IS D_1000025333.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-JUL-05
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL41XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39423
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5
REMARK 200 DATA REDUNDANCY : 4.900
REMARK 200 R MERGE (I) : 0.06100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.52
REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8
REMARK 200 DATA REDUNDANCY IN SHELL : 3.30
REMARK 200 R MERGE FOR SHELL (I) : 0.33400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 2DET
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 71.94
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.38
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES-NA BUFFER (PH 7.5), 1.3
REMARK 280 -1.5M LITHIUM SULFATE, 2.5MM ATP, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
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+1/2,Y+1/2,Z
REMARK 290 4555 -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 119.02750
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.06650
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 119.02750
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 51.06650
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: C, A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, B
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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 C C 75
REMARK 465 A C 76
REMARK 465 C D 75
REMARK 465 A D 76
REMARK 465 MET A -11
REMARK 465 ARG A -10
REMARK 465 GLY A -9
REMARK 465 SER A -8
REMARK 465 HIS A -7
REMARK 465 HIS A -6
REMARK 465 HIS A -5
REMARK 465 HIS A -4
REMARK 465 HIS A -3
REMARK 465 HIS A -2
REMARK 465 GLY A -1
REMARK 465 SER A 0
REMARK 465 MET A 1
REMARK 465 SER A 2
REMARK 465 GLU A 3
REMARK 465 THR A 4
REMARK 465 MET B -11
REMARK 465 ARG B -10
REMARK 465 GLY B -9
REMARK 465 SER B -8
REMARK 465 HIS B -7
REMARK 465 HIS B -6
REMARK 465 HIS B -5
REMARK 465 HIS B -4
REMARK 465 HIS B -3
REMARK 465 HIS B -2
REMARK 465 GLY B -1
REMARK 465 SER B 0
REMARK 465 MET B 1
REMARK 465 SER B 2
REMARK 465 GLU B 3
REMARK 465 THR B 4
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 O2' C D 9 O2' A D 45 2.18
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 C 1 P G C 1 OP3 -0.085
REMARK 500 G D 1 P G D 1 OP3 -0.086
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 G C 18 N9 - C1' - C2' ANGL. DEV. = 9.0 DEGREES
REMARK 500 U C 34 C2' - C3' - O3' ANGL. DEV. = 10.1 DEGREES
REMARK 500 G D 18 N9 - C1' - C2' ANGL. DEV. = 8.8 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 ASP A 17 -83.30 -49.53
REMARK 500 SER A 18 -68.92 -19.64
REMARK 500 SER A 19 -73.55 -37.03
REMARK 500 GLN A 28 -2.66 -51.60
REMARK 500 TYR A 30 148.20 -8.94
REMARK 500 GLU A 42 138.23 -39.32
REMARK 500 TYR A 48 -86.40 -50.53
REMARK 500 CYS A 49 -56.18 -25.37
REMARK 500 ALA A 60 -13.04 -41.24
REMARK 500 VAL A 82 -78.28 -131.10
REMARK 500 ALA A 88 -81.38 -55.10
REMARK 500 ASN A 97 79.97 -107.57
REMARK 500 ILE A 106 -86.42 -128.41
REMARK 500 LYS A 107 -12.39 -39.58
REMARK 500 LYS A 109 -86.87 -156.90
REMARK 500 PHE A 111 -79.12 -62.25
REMARK 500 LEU A 112 -44.58 -27.25
REMARK 500 PHE A 114 -3.07 -51.28
REMARK 500 ASP A 118 -82.59 -130.09
REMARK 500 TYR A 123 113.96 -176.66
REMARK 500 LEU A 142 132.96 -174.00
REMARK 500 LEU A 145 -164.19 -75.62
REMARK 500 SER A 147 -70.80 -9.55
REMARK 500 GLU A 161 -72.47 -43.60
REMARK 500 LEU A 173 -160.83 -70.21
REMARK 500 LYS A 175 -50.23 -26.54
REMARK 500 LYS A 191 52.28 81.57
REMARK 500 LYS A 193 100.79 -29.19
REMARK 500 ASP A 194 -30.65 -29.99
REMARK 500 SER A 195 144.49 104.61
REMARK 500 ILE A 198 137.08 -36.99
REMARK 500 PHE A 200 -37.69 84.61
REMARK 500 GLU A 203 23.99 -70.07
REMARK 500 ARG A 204 170.03 -55.29
REMARK 500 PHE A 206 -75.14 -43.14
REMARK 500 ARG A 207 -43.81 -28.04
REMARK 500 PRO A 215 -157.55 -64.73
REMARK 500 ALA A 216 84.41 -163.90
REMARK 500 PRO A 218 -157.47 -51.14
REMARK 500 ASP A 225 48.83 -108.90
REMARK 500 GLU A 228 158.01 -46.84
REMARK 500 ILE A 229 -39.78 -168.43
REMARK 500 HIS A 232 7.94 -63.01
REMARK 500 GLN A 233 92.69 -14.52
REMARK 500 LEU A 235 -41.46 -164.31
REMARK 500 THR A 239 144.89 -173.80
REMARK 500 LYS A 252 -67.09 9.93
REMARK 500 GLU A 253 52.55 -105.77
REMARK 500 THR A 255 20.56 -60.31
REMARK 500 GLU A 256 -9.49 61.57
REMARK 500
REMARK 500 THIS ENTRY HAS 147 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 G C 17 0.06 SIDE CHAIN
REMARK 500 C C 47 0.07 SIDE CHAIN
REMARK 500 U C 60 0.08 SIDE CHAIN
REMARK 500 G D 17 0.06 SIDE CHAIN
REMARK 500 G D 18 0.05 SIDE CHAIN
REMARK 500 C D 47 0.07 SIDE CHAIN
REMARK 500 U D 60 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 5001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 5002
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP C 134
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP D 134
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2DER RELATED DB: PDB
REMARK 900 THE SAME PROTEIN/TRNA COMPLEX IN THE INITIAL TRNA BINDING STATE
REMARK 900 RELATED ID: 2DET RELATED DB: PDB
REMARK 900 THE SAME PROTEIN/TRNA COMPLEX IN THE PRE-REACTION STATE
DBREF 2DEU A 1 368 UNP P25745 TRMU_ECOLI 1 368
DBREF 2DEU B 1 368 UNP P25745 TRMU_ECOLI 1 368
DBREF 2DEU C 1 76 PDB 2DEU 2DEU 1 76
DBREF 2DEU D 1 76 PDB 2DEU 2DEU 1 76
SEQADV 2DEU MET A -11 UNP P25745 EXPRESSION TAG
SEQADV 2DEU ARG A -10 UNP P25745 EXPRESSION TAG
SEQADV 2DEU GLY A -9 UNP P25745 EXPRESSION TAG
SEQADV 2DEU SER A -8 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS A -7 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS A -6 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS A -5 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS A -4 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS A -3 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS A -2 UNP P25745 EXPRESSION TAG
SEQADV 2DEU GLY A -1 UNP P25745 EXPRESSION TAG
SEQADV 2DEU SER A 0 UNP P25745 EXPRESSION TAG
SEQADV 2DEU MET B -11 UNP P25745 EXPRESSION TAG
SEQADV 2DEU ARG B -10 UNP P25745 EXPRESSION TAG
SEQADV 2DEU GLY B -9 UNP P25745 EXPRESSION TAG
SEQADV 2DEU SER B -8 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS B -7 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS B -6 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS B -5 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS B -4 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS B -3 UNP P25745 EXPRESSION TAG
SEQADV 2DEU HIS B -2 UNP P25745 EXPRESSION TAG
SEQADV 2DEU GLY B -1 UNP P25745 EXPRESSION TAG
SEQADV 2DEU SER B 0 UNP P25745 EXPRESSION TAG
SEQRES 1 C 76 G U C C C C U U C G U C U
SEQRES 2 C 76 A G A G G C C C A G G A C
SEQRES 3 C 76 A C C G C C C U U U C A C
SEQRES 4 C 76 G G C G G U A A C A G G G
SEQRES 5 C 76 G U U C G A A U C C C C U
SEQRES 6 C 76 A G G G G A C G C C A
SEQRES 1 D 76 G U C C C C U U C G U C U
SEQRES 2 D 76 A G A G G C C C A G G A C
SEQRES 3 D 76 A C C G C C C U U U C A C
SEQRES 4 D 76 G G C G G U A A C A G G G
SEQRES 5 D 76 G U U C G A A U C C C C U
SEQRES 6 D 76 A G G G G A C G C C A
SEQRES 1 A 380 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET
SEQRES 2 A 380 SER GLU THR ALA LYS LYS VAL ILE VAL GLY MET SER GLY
SEQRES 3 A 380 GLY VAL ASP SER SER VAL SER ALA TRP LEU LEU GLN GLN
SEQRES 4 A 380 GLN GLY TYR GLN VAL GLU GLY LEU PHE MET LYS ASN TRP
SEQRES 5 A 380 GLU GLU ASP ASP GLY GLU GLU TYR CYS THR ALA ALA ALA
SEQRES 6 A 380 ASP LEU ALA ASP ALA GLN ALA VAL CYS ASP LYS LEU GLY
SEQRES 7 A 380 ILE GLU LEU HIS THR VAL ASN PHE ALA ALA GLU TYR TRP
SEQRES 8 A 380 ASP ASN VAL PHE GLU LEU PHE LEU ALA GLU TYR LYS ALA
SEQRES 9 A 380 GLY ARG THR PRO ASN PRO ASP ILE LEU CYS ASN LYS GLU
SEQRES 10 A 380 ILE LYS PHE LYS ALA PHE LEU GLU PHE ALA ALA GLU ASP
SEQRES 11 A 380 LEU GLY ALA ASP TYR ILE ALA THR GLY HIS TYR VAL ARG
SEQRES 12 A 380 ARG ALA ASP VAL ASP GLY LYS SER ARG LEU LEU ARG GLY
SEQRES 13 A 380 LEU ASP SER ASN LYS ASP GLN SER TYR PHE LEU TYR THR
SEQRES 14 A 380 LEU SER HIS GLU GLN ILE ALA GLN SER LEU PHE PRO VAL
SEQRES 15 A 380 GLY GLU LEU GLU LYS PRO GLN VAL ARG LYS ILE ALA GLU
SEQRES 16 A 380 ASP LEU GLY LEU VAL THR ALA LYS LYS LYS ASP SER THR
SEQRES 17 A 380 GLY ILE CYS PHE ILE GLY GLU ARG LYS PHE ARG GLU PHE
SEQRES 18 A 380 LEU GLY ARG TYR LEU PRO ALA GLN PRO GLY LYS ILE ILE
SEQRES 19 A 380 THR VAL ASP GLY ASP GLU ILE GLY GLU HIS GLN GLY LEU
SEQRES 20 A 380 MET TYR HIS THR LEU GLY GLN ARG LYS GLY LEU GLY ILE
SEQRES 21 A 380 GLY GLY THR LYS GLU GLY THR GLU GLU PRO TRP TYR VAL
SEQRES 22 A 380 VAL ASP LYS ASP VAL GLU ASN ASN ILE LEU VAL VAL ALA
SEQRES 23 A 380 GLN GLY HIS GLU HIS PRO ARG LEU MET SER VAL GLY LEU
SEQRES 24 A 380 ILE ALA GLN GLN LEU HIS TRP VAL ASP ARG GLU PRO PHE
SEQRES 25 A 380 THR GLY THR MET ARG CYS THR VAL LYS THR ARG TYR ARG
SEQRES 26 A 380 GLN THR ASP ILE PRO CYS THR VAL LYS ALA LEU ASP ASP
SEQRES 27 A 380 ASP ARG ILE GLU VAL ILE PHE ASP GLU PRO VAL ALA ALA
SEQRES 28 A 380 VAL THR PRO GLY GLN SER ALA VAL PHE TYR ASN GLY GLU
SEQRES 29 A 380 VAL CYS LEU GLY GLY GLY ILE ILE GLU GLN ARG LEU PRO
SEQRES 30 A 380 LEU PRO VAL
SEQRES 1 B 380 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET
SEQRES 2 B 380 SER GLU THR ALA LYS LYS VAL ILE VAL GLY MET SER GLY
SEQRES 3 B 380 GLY VAL ASP SER SER VAL SER ALA TRP LEU LEU GLN GLN
SEQRES 4 B 380 GLN GLY TYR GLN VAL GLU GLY LEU PHE MET LYS ASN TRP
SEQRES 5 B 380 GLU GLU ASP ASP GLY GLU GLU TYR CYS THR ALA ALA ALA
SEQRES 6 B 380 ASP LEU ALA ASP ALA GLN ALA VAL CYS ASP LYS LEU GLY
SEQRES 7 B 380 ILE GLU LEU HIS THR VAL ASN PHE ALA ALA GLU TYR TRP
SEQRES 8 B 380 ASP ASN VAL PHE GLU LEU PHE LEU ALA GLU TYR LYS ALA
SEQRES 9 B 380 GLY ARG THR PRO ASN PRO ASP ILE LEU CYS ASN LYS GLU
SEQRES 10 B 380 ILE LYS PHE LYS ALA PHE LEU GLU PHE ALA ALA GLU ASP
SEQRES 11 B 380 LEU GLY ALA ASP TYR ILE ALA THR GLY HIS TYR VAL ARG
SEQRES 12 B 380 ARG ALA ASP VAL ASP GLY LYS SER ARG LEU LEU ARG GLY
SEQRES 13 B 380 LEU ASP SER ASN LYS ASP GLN SER TYR PHE LEU TYR THR
SEQRES 14 B 380 LEU SER HIS GLU GLN ILE ALA GLN SER LEU PHE PRO VAL
SEQRES 15 B 380 GLY GLU LEU GLU LYS PRO GLN VAL ARG LYS ILE ALA GLU
SEQRES 16 B 380 ASP LEU GLY LEU VAL THR ALA LYS LYS LYS ASP SER THR
SEQRES 17 B 380 GLY ILE CYS PHE ILE GLY GLU ARG LYS PHE ARG GLU PHE
SEQRES 18 B 380 LEU GLY ARG TYR LEU PRO ALA GLN PRO GLY LYS ILE ILE
SEQRES 19 B 380 THR VAL ASP GLY ASP GLU ILE GLY GLU HIS GLN GLY LEU
SEQRES 20 B 380 MET TYR HIS THR LEU GLY GLN ARG LYS GLY LEU GLY ILE
SEQRES 21 B 380 GLY GLY THR LYS GLU GLY THR GLU GLU PRO TRP TYR VAL
SEQRES 22 B 380 VAL ASP LYS ASP VAL GLU ASN ASN ILE LEU VAL VAL ALA
SEQRES 23 B 380 GLN GLY HIS GLU HIS PRO ARG LEU MET SER VAL GLY LEU
SEQRES 24 B 380 ILE ALA GLN GLN LEU HIS TRP VAL ASP ARG GLU PRO PHE
SEQRES 25 B 380 THR GLY THR MET ARG CYS THR VAL LYS THR ARG TYR ARG
SEQRES 26 B 380 GLN THR ASP ILE PRO CYS THR VAL LYS ALA LEU ASP ASP
SEQRES 27 B 380 ASP ARG ILE GLU VAL ILE PHE ASP GLU PRO VAL ALA ALA
SEQRES 28 B 380 VAL THR PRO GLY GLN SER ALA VAL PHE TYR ASN GLY GLU
SEQRES 29 B 380 VAL CYS LEU GLY GLY GLY ILE ILE GLU GLN ARG LEU PRO
SEQRES 30 B 380 LEU PRO VAL
HET AMP C 134 22
HET AMP D 134 22
HET SO4 A5001 5
HET SO4 B5002 5
HETNAM AMP ADENOSINE MONOPHOSPHATE
HETNAM SO4 SULFATE ION
FORMUL 5 AMP 2(C10 H14 N5 O7 P)
FORMUL 7 SO4 2(O4 S 2-)
HELIX 1 1 GLY A 15 GLY A 29 1 15
HELIX 2 2 GLY A 45 GLY A 66 1 22
HELIX 3 3 PHE A 74 VAL A 82 1 9
HELIX 4 4 VAL A 82 ALA A 92 1 11
HELIX 5 5 ASN A 97 ASN A 103 1 7
HELIX 6 6 LYS A 109 GLU A 117 1 9
HELIX 7 7 GLN A 151 TYR A 156 5 6
HELIX 8 8 SER A 159 GLN A 165 1 7
HELIX 9 9 PRO A 169 LEU A 173 5 5
HELIX 10 10 GLU A 174 GLY A 186 1 13
HELIX 11 11 LYS A 205 GLY A 211 1 7
HELIX 12 12 HIS A 279 ARG A 281 5 3
HELIX 13 13 GLY B 15 GLY B 29 1 15
HELIX 14 14 GLY B 45 GLY B 66 1 22
HELIX 15 15 PHE B 74 VAL B 82 1 9
HELIX 16 16 VAL B 82 ALA B 92 1 11
HELIX 17 17 ASN B 97 ASN B 103 1 7
HELIX 18 18 LYS B 109 GLU B 117 1 9
HELIX 19 19 GLN B 151 TYR B 156 5 6
HELIX 20 20 SER B 159 GLN B 165 1 7
HELIX 21 21 PRO B 169 LEU B 173 5 5
HELIX 22 22 GLU B 174 GLY B 186 1 13
HELIX 23 23 LYS B 205 GLY B 211 1 7
HELIX 24 24 HIS B 279 ARG B 281 5 3
SHEET 1 A 5 LEU A 69 VAL A 72 0
SHEET 2 A 5 GLN A 31 MET A 37 1 N PHE A 36 O HIS A 70
SHEET 3 A 5 LYS A 7 GLY A 11 1 N VAL A 8 O GLU A 33
SHEET 4 A 5 ILE A 124 ALA A 125 1 O ALA A 125 N GLY A 11
SHEET 5 A 5 SER A 166 LEU A 167 1 O LEU A 167 N ILE A 124
SHEET 1 B 2 VAL A 130 VAL A 135 0
SHEET 2 B 2 LYS A 138 ARG A 143 -1 O LYS A 138 N VAL A 135
SHEET 1 C 2 LYS A 220 ILE A 222 0
SHEET 2 C 2 GLU A 228 GLU A 231 -1 O GLY A 230 N ILE A 221
SHEET 1 D 2 VAL A 261 ASP A 265 0
SHEET 2 D 2 ILE A 270 VAL A 273 -1 O VAL A 272 N ASP A 263
SHEET 1 E 7 CYS A 354 GLY A 356 0
SHEET 2 E 7 PHE A 348 TYR A 349 -1 N PHE A 348 O LEU A 355
SHEET 3 E 7 THR A 303 VAL A 308 -1 N THR A 307 O TYR A 349
SHEET 4 E 7 ILE A 317 ALA A 323 -1 O VAL A 321 N MET A 304
SHEET 5 E 7 ILE A 329 ALA A 338 -1 O GLU A 330 N LYS A 322
SHEET 6 E 7 MET A 283 ALA A 289 -1 N SER A 284 O VAL A 337
SHEET 7 E 7 ILE A 360 PRO A 365 -1 O GLN A 362 N ILE A 288
SHEET 1 F 5 LEU B 69 VAL B 72 0
SHEET 2 F 5 GLN B 31 MET B 37 1 N PHE B 36 O HIS B 70
SHEET 3 F 5 LYS B 7 GLY B 11 1 N VAL B 8 O GLU B 33
SHEET 4 F 5 ILE B 124 ALA B 125 1 O ALA B 125 N GLY B 11
SHEET 5 F 5 SER B 166 LEU B 167 1 O LEU B 167 N ILE B 124
SHEET 1 G 2 VAL B 130 VAL B 135 0
SHEET 2 G 2 LYS B 138 ARG B 143 -1 O LYS B 138 N VAL B 135
SHEET 1 H 2 LYS B 220 ILE B 222 0
SHEET 2 H 2 GLU B 228 GLU B 231 -1 O GLY B 230 N ILE B 221
SHEET 1 I 2 VAL B 261 ASP B 265 0
SHEET 2 I 2 ILE B 270 VAL B 273 -1 O VAL B 272 N ASP B 263
SHEET 1 J 7 VAL B 337 ALA B 338 0
SHEET 2 J 7 MET B 283 ALA B 289 -1 N SER B 284 O VAL B 337
SHEET 3 J 7 ILE B 329 VAL B 331 -1 O VAL B 331 N LEU B 287
SHEET 4 J 7 ILE B 317 ALA B 323 -1 N LYS B 322 O GLU B 330
SHEET 5 J 7 THR B 303 VAL B 308 -1 N MET B 304 O VAL B 321
SHEET 6 J 7 PHE B 348 TYR B 349 -1 O TYR B 349 N THR B 307
SHEET 7 J 7 CYS B 354 GLY B 356 -1 O LEU B 355 N PHE B 348
SHEET 1 K 3 VAL B 337 ALA B 338 0
SHEET 2 K 3 MET B 283 ALA B 289 -1 N SER B 284 O VAL B 337
SHEET 3 K 3 ILE B 360 PRO B 365 -1 O GLN B 362 N ILE B 288
LINK O2 U C 34 P AMP C 134 1555 1555 1.73
LINK O2 U D 34 P AMP D 134 1555 1555 1.72
SITE 1 AC1 6 SER A 13 GLY A 15 VAL A 16 ASP A 17
SITE 2 AC1 6 SER A 18 AMP C 134
SITE 1 AC2 6 SER B 13 GLY B 15 VAL B 16 ASP B 17
SITE 2 AC2 6 SER B 18 AMP D 134
SITE 1 AC3 12 GLY A 11 MET A 12 SER A 13 SER A 18
SITE 2 AC3 12 LEU A 35 PHE A 36 MET A 37 THR A 126
SITE 3 AC3 12 GLY A 127 HIS A 128 SO4 A5001 U C 34
SITE 1 AC4 13 GLY B 11 MET B 12 SER B 13 SER B 18
SITE 2 AC4 13 LEU B 35 PHE B 36 MET B 37 THR B 126
SITE 3 AC4 13 GLY B 127 HIS B 128 PHE B 200 SO4 B5002
SITE 4 AC4 13 U D 34
CRYST1 238.055 102.133 108.158 90.00 117.03 90.00 C 1 2 1 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.004201 0.000000 0.002143 0.00000
SCALE2 0.000000 0.009791 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010379 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
