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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
