HEADER LYASE/RNA 01-OCT-03 1R3E 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: 5'-R(*CP*UP*GP*UP*GP*UP*(FHU) COMPND 3 P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'; COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*CP*UP*GP*UP*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)- COMPND 8 3'; COMPND 9 CHAIN: D, E; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: TRNA PSEUDOURIDINE SYNTHASE B; COMPND 13 CHAIN: A; COMPND 14 SYNONYM: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, COMPND 15 PSEUDOURIDYLATE SYNTHASE, URACIL HYDROLYASE; COMPND 16 EC: 4.2.1.70; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 7 ORGANISM_TAXID: 2336; SOURCE 8 GENE: TRUB; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS RNA MODIFICATION, PSEUDOURIDYLATION, LYASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.PAN,S.AGARWALLA,D.T.MOUSTAKAS,J.FINER-MOORE,R.M.STROUD REVDAT 4 07-FEB-18 1R3E 1 REMARK REVDAT 3 16-NOV-11 1R3E 1 VERSN HETATM REVDAT 2 24-FEB-09 1R3E 1 VERSN REVDAT 1 04-NOV-03 1R3E 0 JRNL AUTH H.PAN,S.AGARWALLA,D.T.MOUSTAKAS,J.FINER-MOORE,R.M.STROUD JRNL TITL CRYSTAL STRUCTURE OF TRNA PSEUDOURIDINE SYNTHASE TRUB AND JRNL TITL 2 ITS RNA COMPLEX: RNA RECOGNITION THROUGH A COMBINATION OF JRNL TITL 3 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 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.100 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 38642 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) : 0.223 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1159 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL 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 : 2459 REMARK 3 NUCLEIC ACID ATOMS : 1067 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 263 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.360 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 1R3E 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_1000020387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-02 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 : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9730, 0.9796, 0.9800, 1.1271 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL 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 : 38642 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 63.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MAGNESIUM SULFATE, REMARK 280 SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP 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 49.43100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 79.66850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.43100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 79.66850 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, E, 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 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 HOH A 386 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 494 LIES ON A SPECIAL POSITION. 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 HIS A 302 REMARK 465 GLU A 303 REMARK 465 ARG A 304 REMARK 465 ASN A 305 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 O HOH C 29 O HOH A 373 1.68 REMARK 500 O LEU A 299 NE ARG A 300 1.75 REMARK 500 OE1 GLU A 290 OG1 THR A 310 1.95 REMARK 500 O ALA A 51 O HOH A 408 2.04 REMARK 500 O HOH C 29 O HOH C 125 2.04 REMARK 500 O HOH C 133 O HOH A 337 2.11 REMARK 500 O ASP A 48 O HOH A 408 2.13 REMARK 500 O HOH C 125 O HOH A 373 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 388 O HOH A 480 2656 0.17 REMARK 500 O HOH C 205 O HOH C 212 2656 0.51 REMARK 500 O HOH C 133 O HOH C 247 2656 0.65 REMARK 500 O HOH C 41 O HOH C 41 2655 1.99 REMARK 500 N3 U C 414 N3 U C 414 2656 2.17 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 A D 419 C2' A D 419 O2' -0.134 REMARK 500 A D 419 N7 A D 419 C8 0.046 REMARK 500 TRP A 77 NE1 TRP A 77 CE2 0.114 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 FHU C 410 O3' - P - O5' ANGL. DEV. = 22.2 DEGREES REMARK 500 FHU C 410 O3' - P - OP1 ANGL. DEV. = -21.7 DEGREES REMARK 500 A D 419 C1' - C2' - O2' ANGL. DEV. = 25.5 DEGREES REMARK 500 A D 419 C3' - C2' - O2' ANGL. DEV. = -33.3 DEGREES REMARK 500 A D 419 N1 - C2 - N3 ANGL. DEV. = -4.3 DEGREES REMARK 500 A D 419 C2 - N3 - C4 ANGL. DEV. = 6.3 DEGREES REMARK 500 A D 419 N3 - C4 - C5 ANGL. DEV. = -5.3 DEGREES REMARK 500 A D 419 C5 - C6 - N1 ANGL. DEV. = 4.9 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 ASN A 60 -128.05 50.04 REMARK 500 GLU A 105 -32.24 -29.55 REMARK 500 LYS A 157 147.34 -170.38 REMARK 500 GLU A 164 100.31 177.44 REMARK 500 CYS A 193 -2.01 -164.54 REMARK 500 GLN A 245 -3.24 -46.34 REMARK 500 LEU A 252 -8.97 -59.14 REMARK 500 LEU A 262 -149.39 -165.14 REMARK 500 LYS A 263 -88.12 164.26 REMARK 500 PHE A 268 114.55 -163.99 REMARK 500 LYS A 270 136.12 -38.95 REMARK 500 GLU A 279 -7.57 57.23 REMARK 500 SER A 294 -18.15 -168.12 REMARK 500 LEU A 299 -1.32 -48.41 REMARK 500 ARG A 300 -116.05 -149.22 REMARK 500 ARG A 307 115.83 -14.16 REMARK 500 VAL A 308 -58.57 -137.76 REMARK 500 THR A 317 97.50 31.70 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 408 0.05 SIDE CHAIN REMARK 500 G D 408 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R3F 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 1R3E A 10 318 UNP Q9WZW0 TRUB_THEMA 1 309 DBREF 1R3E C 404 420 PDB 1R3E 1R3E 404 420 DBREF 1R3E D 404 420 PDB 1R3E 1R3E 404 420 DBREF 1R3E E 404 420 PDB 1R3E 1R3E 404 420 SEQRES 1 C 17 C U G U G U FHU C G A U C C SEQRES 2 C 17 A C A G SEQRES 1 D 17 C U G U G U U C G A U C C SEQRES 2 D 17 A C A G SEQRES 1 E 17 C U G U G U U C G A U C C SEQRES 2 E 17 A C A G SEQRES 1 A 309 MET LYS HIS GLY ILE LEU VAL ALA TYR LYS PRO LYS GLY SEQRES 2 A 309 PRO THR SER HIS ASP VAL VAL ASP GLU VAL ARG LYS LYS SEQRES 3 A 309 LEU LYS THR ARG LYS VAL GLY HIS GLY GLY THR LEU ASP SEQRES 4 A 309 PRO PHE ALA CYS GLY VAL LEU ILE ILE GLY VAL ASN GLN SEQRES 5 A 309 GLY THR ARG ILE LEU GLU PHE TYR LYS ASP LEU LYS LYS SEQRES 6 A 309 VAL TYR TRP VAL LYS MET ARG LEU GLY LEU ILE THR GLU SEQRES 7 A 309 THR PHE ASP ILE THR GLY GLU VAL VAL GLU GLU ARG GLU SEQRES 8 A 309 CYS ASN VAL THR GLU GLU GLU ILE ARG GLU ALA ILE PHE SEQRES 9 A 309 SER PHE VAL GLY GLU TYR ASP GLN VAL PRO PRO ALA TYR SEQRES 10 A 309 SER ALA LYS LYS TYR LYS GLY GLU ARG LEU TYR LYS LEU SEQRES 11 A 309 ALA ARG GLU GLY LYS ILE ILE ASN LEU PRO PRO LYS ARG SEQRES 12 A 309 VAL LYS ILE PHE LYS ILE TRP ASP VAL ASN ILE GLU GLY SEQRES 13 A 309 ARG ASP VAL SER PHE ARG VAL GLU VAL SER PRO GLY THR SEQRES 14 A 309 TYR ILE ARG SER LEU CYS MET ASP ILE GLY TYR LYS LEU SEQRES 15 A 309 GLY CYS GLY ALA THR ALA VAL GLU LEU VAL ARG GLU SER SEQRES 16 A 309 VAL GLY PRO HIS THR ILE GLU GLU SER LEU ASN VAL PHE SEQRES 17 A 309 GLU ALA ALA PRO GLU GLU ILE GLU ASN ARG ILE ILE PRO SEQRES 18 A 309 LEU GLU LYS CYS LEU GLU TRP LEU PRO ARG VAL VAL VAL SEQRES 19 A 309 HIS GLN GLU SER THR LYS MET ILE LEU ASN GLY SER GLN SEQRES 20 A 309 ILE HIS LEU GLU MET LEU LYS GLU TRP ASP GLY PHE LYS SEQRES 21 A 309 LYS GLY GLU VAL VAL ARG VAL PHE ASN GLU GLU GLY ARG SEQRES 22 A 309 LEU LEU ALA LEU ALA GLU ALA GLU ARG ASN SER SER PHE SEQRES 23 A 309 LEU GLU THR LEU ARG LYS HIS GLU ARG ASN GLU ARG VAL SEQRES 24 A 309 LEU THR LEU ARG LYS VAL PHE ASN THR ARG MODRES 1R3E FHU C 410 U HET FHU C 410 22 HETNAM FHU (5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5'- HETNAM 2 FHU MONOPHOSPHATE FORMUL 1 FHU C9 H14 F N2 O10 P FORMUL 5 HOH *263(H2 O) HELIX 1 1 THR A 24 LEU A 36 1 13 HELIX 2 2 GLN A 61 LYS A 70 5 10 HELIX 3 3 THR A 104 SER A 114 1 11 HELIX 4 4 LEU A 136 GLU A 142 1 7 HELIX 5 5 TYR A 179 LEU A 191 1 13 HELIX 6 6 GLU A 211 SER A 213 5 3 HELIX 7 7 ALA A 220 ILE A 228 1 9 HELIX 8 8 GLU A 232 CYS A 234 5 3 HELIX 9 9 SER A 247 LEU A 252 1 6 SHEET 1 A 4 VAL A 41 HIS A 43 0 SHEET 2 A 4 CYS A 52 VAL A 59 -1 O GLY A 58 N GLY A 42 SHEET 3 A 4 ALA A 195 VAL A 205 1 O ARG A 202 N CYS A 52 SHEET 4 A 4 HIS A 208 THR A 209 -1 O HIS A 208 N VAL A 205 SHEET 1 B 8 GLY A 117 GLN A 121 0 SHEET 2 B 8 LYS A 151 GLU A 164 -1 O VAL A 153 N TYR A 119 SHEET 3 B 8 ASP A 167 VAL A 174 -1 O ARG A 171 N TRP A 159 SHEET 4 B 8 LYS A 74 LEU A 82 -1 N MET A 80 O VAL A 168 SHEET 5 B 8 ALA A 195 VAL A 205 -1 O VAL A 198 N LYS A 79 SHEET 6 B 8 CYS A 52 VAL A 59 1 N CYS A 52 O ARG A 202 SHEET 7 B 8 GLY A 13 LYS A 19 -1 N LEU A 15 O ILE A 57 SHEET 8 B 8 ILE A 229 PRO A 230 -1 O ILE A 229 N ILE A 14 SHEET 1 C 2 LEU A 84 THR A 86 0 SHEET 2 C 2 VAL A 95 GLU A 98 -1 O VAL A 96 N ILE A 85 SHEET 1 D 2 LYS A 130 TYR A 131 0 SHEET 2 D 2 GLU A 134 ARG A 135 -1 O GLU A 134 N TYR A 131 SHEET 1 E 6 ILE A 257 HIS A 258 0 SHEET 2 E 6 ARG A 307 VAL A 314 -1 O VAL A 308 N ILE A 257 SHEET 3 E 6 LEU A 283 ALA A 289 -1 N GLU A 288 O THR A 310 SHEET 4 E 6 VAL A 273 PHE A 277 -1 N VAL A 274 O ALA A 287 SHEET 5 E 6 ARG A 240 VAL A 242 1 N VAL A 241 O PHE A 277 SHEET 6 E 6 GLU A 264 TRP A 265 -1 O GLU A 264 N VAL A 242 SSBOND 1 CYS A 101 CYS A 193 1555 1555 2.03 LINK O3' U C 409 P FHU C 410 1555 1555 1.55 CRYST1 98.862 159.337 44.545 90.00 97.77 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 0.010120 0.000000 0.001380 0.00000 SCALE2 0.000000 0.006280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022660 0.00000