HEADER LYASE 01-OCT-03 1R3F
TITLE CRYSTAL STRUCTURE OF TRNA PSEUDOURIDINE SYNTHASE TRUB AND
TITLE 2 ITS RNA COMPLEX: RNA-PROTEIN RECOGNITION THROUGH A
TITLE 3 COMBINATION OF RIGID DOCKING AND INDUCED FIT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRNA PSEUDOURIDINE SYNTHASE B;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE,
COMPND 5 PSEUDOURIDYLATE SYNTHASE, URACIL HYDROLYASE, P35 PROTEIN;
COMPND 6 EC: 4.2.1.70;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 GENE: TRUB;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B
KEYWDS RNA MODIFICATION, PSEUDOURIDYLATION, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.PAN,S.AGARWALLA,D.T.MOUSTAKAS,J.FINER-MOORE,R.M.STROUD
REVDAT 2 24-FEB-09 1R3F 1 VERSN
REVDAT 1 04-NOV-03 1R3F 0
JRNL AUTH H.PAN,S.AGARWALLA,D.T.MOUSTAKAS,J.FINER-MOORE,
JRNL AUTH 2 R.M.STROUD
JRNL TITL STRUCTURE OF TRNA PSEUDOURIDINE SYNTHASE TRUB AND
JRNL TITL 2 ITS RNA COMPLEX: RNA RECOGNITION THROUGH A
JRNL TITL 3 COMBINATION OF RIGID DOCKING AND INDUCED FIT
JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 12648 2003
JRNL REFN ISSN 0027-8424
JRNL PMID 14566049
JRNL DOI 10.1073/PNAS.2135585100
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.85 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) : 1.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.850
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 48520
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.228
REMARK 3 FREE R VALUE : 0.257
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 2425
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) : 1.85
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2280
REMARK 3 BIN FREE R VALUE : 0.2570
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
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 : 2158
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
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) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 BOND ANGLES (DEGREES) : 1.29
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
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 1R3F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-03.
REMARK 100 THE RCSB ID CODE IS RCSB020388.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-JUN-01
REMARK 200 TEMPERATURE (KELVIN) : 298.0
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ALS
REMARK 200 BEAMLINE : 5.0.2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97926, 0.97942, 0.9610
REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111)
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24806
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850
REMARK 200 RESOLUTION RANGE LOW (A) : 40.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 9.970
REMARK 200 R MERGE (I) : 0.06900
REMARK 200 R SYM (I) : 0.06900
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.47000
REMARK 200 R SYM FOR SHELL (I) : 0.47000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.07
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4K, MAGNESIUM SULFATE, SODIUM
REMARK 280 CACODYLATE , PH 6.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 323.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 35.50500
REMARK 290 SMTRY3 2 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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (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 MET A 1
REMARK 465 SER A 2
REMARK 465 ARG A 3
REMARK 465 PRO A 4
REMARK 465 ARG A 5
REMARK 465 ARG A 6
REMARK 465 ARG A 7
REMARK 465 SER A 124
REMARK 465 MET A 125
REMARK 465 TYR A 126
REMARK 465 SER A 127
REMARK 465 ALA A 128
REMARK 465 LEU A 129
REMARK 465 LYS A 130
REMARK 465 TYR A 131
REMARK 465 GLN A 132
REMARK 465 GLY A 133
REMARK 465 LYS A 134
REMARK 465 LYS A 135
REMARK 465 LEU A 136
REMARK 465 TYR A 137
REMARK 465 GLU A 138
REMARK 465 TYR A 139
REMARK 465 ALA A 140
REMARK 465 ARG A 141
REMARK 465 GLN A 142
REMARK 465 GLY A 143
REMARK 465 ILE A 144
REMARK 465 GLU A 145
REMARK 465 VAL A 146
REMARK 465 PRO A 147
REMARK 465 ARG A 148
REMARK 465 GLU A 149
REMARK 465 ALA A 150
REMARK 465 ARG A 151
REMARK 465 PRO A 152
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 87 41.62 -86.19
REMARK 500 THR A 88 -11.27 -167.12
REMARK 500 GLU A 97 118.67 -161.66
REMARK 500 ILE A 122 77.56 -158.17
REMARK 500 SER A 206 -145.30 54.49
REMARK 500 PRO A 276 -178.78 -54.28
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1R3E RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF TRNA PSEUDOURIDINE SYNTHASE TRUB AND
REMARK 900 ITS RNA COMPLEX: RNA-PROTEIN RECOGNITION THROUGH A
REMARK 900 COMBINATION OF RIGID DOCKING AND INDUCED FIT
DBREF 1R3F A 1 314 UNP P60340 TRUB_ECOLI 1 314
SEQRES 1 A 314 MET SER ARG PRO ARG ARG ARG GLY ARG ASP ILE ASN GLY
SEQRES 2 A 314 VAL LEU LEU LEU ASP LYS PRO GLN GLY MET SER SER ASN
SEQRES 3 A 314 ASP ALA LEU GLN LYS VAL LYS ARG ILE TYR ASN ALA ASN
SEQRES 4 A 314 ARG ALA GLY HIS THR GLY ALA LEU ASP PRO LEU ALA THR
SEQRES 5 A 314 GLY MET LEU PRO ILE CYS LEU GLY GLU ALA THR LYS PHE
SEQRES 6 A 314 SER GLN TYR LEU LEU ASP SER ASP LYS ARG TYR ARG VAL
SEQRES 7 A 314 ILE ALA ARG LEU GLY GLN ARG THR ASP THR SER ASP ALA
SEQRES 8 A 314 ASP GLY GLN ILE VAL GLU GLU ARG PRO VAL THR PHE SER
SEQRES 9 A 314 ALA GLU GLN LEU ALA ALA ALA LEU ASP THR PHE ARG GLY
SEQRES 10 A 314 ASP ILE GLU GLN ILE PRO SER MET TYR SER ALA LEU LYS
SEQRES 11 A 314 TYR GLN GLY LYS LYS LEU TYR GLU TYR ALA ARG GLN GLY
SEQRES 12 A 314 ILE GLU VAL PRO ARG GLU ALA ARG PRO ILE THR VAL TYR
SEQRES 13 A 314 GLU LEU LEU PHE ILE ARG HIS GLU GLY ASN GLU LEU GLU
SEQRES 14 A 314 LEU GLU ILE HIS CYS SER LYS GLY THR TYR ILE ARG THR
SEQRES 15 A 314 ILE ILE ASP ASP LEU GLY GLU LYS LEU GLY CYS GLY ALA
SEQRES 16 A 314 HIS VAL ILE TYR LEU ARG ARG LEU ALA VAL SER LYS TYR
SEQRES 17 A 314 PRO VAL GLU ARG MET VAL THR LEU GLU HIS LEU ARG GLU
SEQRES 18 A 314 LEU VAL GLU GLN ALA GLU GLN GLN ASP ILE PRO ALA ALA
SEQRES 19 A 314 GLU LEU LEU ASP PRO LEU LEU MET PRO MET ASP SER PRO
SEQRES 20 A 314 ALA SER ASP TYR PRO VAL VAL ASN LEU PRO LEU THR SER
SEQRES 21 A 314 SER VAL TYR PHE LYS ASN GLY ASN PRO VAL ARG THR SER
SEQRES 22 A 314 GLY ALA PRO LEU GLU GLY LEU VAL ARG VAL THR GLU GLY
SEQRES 23 A 314 GLU ASN GLY LYS PHE ILE GLY MET GLY GLU ILE ASP ASP
SEQRES 24 A 314 GLU GLY ARG VAL ALA PRO ARG ARG LEU VAL VAL GLU TYR
SEQRES 25 A 314 PRO ALA
HELIX 1 1 SER A 24 TYR A 36 1 13
HELIX 2 2 GLU A 61 PHE A 65 5 5
HELIX 3 3 SER A 66 ASP A 71 1 6
HELIX 4 4 SER A 104 THR A 114 1 11
HELIX 5 5 TYR A 179 LEU A 191 1 13
HELIX 6 6 PRO A 209 MET A 213 5 5
HELIX 7 7 THR A 215 ASP A 230 1 16
HELIX 8 8 PRO A 232 ASP A 238 1 7
HELIX 9 9 PRO A 239 LEU A 241 5 3
HELIX 10 10 ASP A 245 SER A 249 5 5
HELIX 11 11 PRO A 257 ASN A 266 1 10
SHEET 1 A 3 GLY A 13 LYS A 19 0
SHEET 2 A 3 THR A 52 LEU A 59 -1 O LEU A 59 N GLY A 13
SHEET 3 A 3 ALA A 41 HIS A 43 -1 N GLY A 42 O CYS A 58
SHEET 1 B 7 GLY A 13 LYS A 19 0
SHEET 2 B 7 THR A 52 LEU A 59 -1 O LEU A 59 N GLY A 13
SHEET 3 B 7 ALA A 195 VAL A 205 1 O ARG A 202 N THR A 52
SHEET 4 B 7 LYS A 74 LEU A 82 -1 N ARG A 81 O HIS A 196
SHEET 5 B 7 GLU A 167 CYS A 174 -1 O LEU A 168 N ALA A 80
SHEET 6 B 7 THR A 154 GLU A 164 -1 N ARG A 162 O GLU A 169
SHEET 7 B 7 GLY A 117 ASP A 118 -1 N GLY A 117 O VAL A 155
SHEET 1 C 2 GLN A 84 THR A 86 0
SHEET 2 C 2 ILE A 95 GLU A 98 -1 O VAL A 96 N ARG A 85
SHEET 1 D 4 VAL A 253 LEU A 256 0
SHEET 2 D 4 LEU A 280 GLU A 285 1 O ARG A 282 N VAL A 254
SHEET 3 D 4 LYS A 290 ILE A 297 -1 O GLY A 295 N VAL A 281
SHEET 4 D 4 VAL A 303 LEU A 308 -1 O ARG A 307 N MET A 294
CRYST1 48.030 71.010 48.670 90.00 117.87 90.00 P 1 21 1 2
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 0.020820 0.000000 0.011010 0.00000
SCALE2 0.000000 0.014083 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023242 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
