HEADER LYASE 01-OCT-03 1R3F TITLE CRYSTAL STRUCTURE OF TRNA PSEUDOURIDINE SYNTHASE TRUB AND ITS RNA TITLE 2 COMPLEX: RNA-PROTEIN RECOGNITION THROUGH A COMBINATION OF RIGID TITLE 3 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 4 14-FEB-24 1R3F 1 REMARK REVDAT 3 07-FEB-18 1R3F 1 REMARK 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,R.M.STROUD JRNL TITL STRUCTURE OF TRNA PSEUDOURIDINE SYNTHASE TRUB AND ITS RNA JRNL TITL 2 COMPLEX: RNA RECOGNITION THROUGH A COMBINATION OF RIGID JRNL TITL 3 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 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) : 1.290 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020388. 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 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 ITS RNA REMARK 900 COMPLEX: RNA-PROTEIN RECOGNITION THROUGH A COMBINATION OF RIGID REMARK 900 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