PDB Short entry for 1K8W HEADER LYASE/RNA 25-OCT-01 1K8W TITLE CRYSTAL STRUCTURE OF THE E. COLI PSEUDOURIDINE SYNTHASE TRUB BOUND TO TITLE 2 A T STEM-LOOP RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU) COMPND 3 P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'; COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: T STEM-LOOP RNA; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TRNA PSEUDOURIDINE SYNTHASE B; COMPND 9 CHAIN: A; COMPND 10 FRAGMENT: RESIDUES 10-314; COMPND 11 SYNONYM: TRUB PSEUDOURIDINE SYNTHASE, TRNA PSEUDOURIDINE 55 SYNTHASE, COMPND 12 PSEUDOURIDYLATE SYNTHASE; COMPND 13 EC: 4.2.1.70; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 5 ORGANISM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-RNA COMPLEX, T STEM-LOOP, TRNA, LYASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.HOANG,A.R.FERRE-D'AMARE REVDAT 4 07-FEB-24 1K8W 1 REMARK LINK REVDAT 3 24-FEB-09 1K8W 1 VERSN REVDAT 2 01-APR-03 1K8W 1 JRNL REVDAT 1 31-DEC-01 1K8W 0 JRNL AUTH C.HOANG,A.R.FERRE-D'AMARE JRNL TITL COCRYSTAL STRUCTURE OF A TRNA PSI55 PSEUDOURIDINE SYNTHASE: JRNL TITL 2 NUCLEOTIDE FLIPPING BY AN RNA-MODIFYING ENZYME. JRNL REF CELL(CAMBRIDGE,MASS.) V. 107 929 2001 JRNL REFN ISSN 0092-8674 JRNL PMID 11779468 JRNL DOI 10.1016/S0092-8674(01)00618-3 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) : 28.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 562571.390 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 34482 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) : 0.184 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3444 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4732 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 526 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2339 REMARK 3 NUCLEIC ACID ATOMS : 466 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.09000 REMARK 3 B22 (A**2) : 5.58000 REMARK 3 B33 (A**2) : -1.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.650 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.690 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.430 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.520 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.600 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 51.28 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA-FHP_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA-FHP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1K8W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-01; 04-JUL-01 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : ALS; ROTATING ANODE REMARK 200 BEAMLINE : 5.0.2; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9611, 0.9792, 0.9794; 1.5418 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL; OSMIC CONFOCAL REMARK 200 MIRROR REMARK 200 OPTICS : MONOCHROMATOR; OSMIC CONFOCAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35366 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 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; SINGLE WAVELENGTH 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 (%): 49.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MAGNESIUM CHLORIDE, REMARK 280 PEG400, HEPES, TCEP, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K 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 72.52700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.18050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.52700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.18050 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 300 REMARK: THE T STEM-LOOP RNA USED IN CRYSTALLIZATION REMARK 300 CONTAINS ALL THE STRUCTURAL DETERMINANTS REMARK 300 EMPLOYED BY TRUB IN MODIFYING INTACT TRNA 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: B, 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 -12 REMARK 465 GLY A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS 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 HIS A -1 REMARK 465 SER A 0 REMARK 465 SER A 1 REMARK 465 GLY A 2 REMARK 465 HIS A 3 REMARK 465 ILE A 4 REMARK 465 GLU A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 HIS A 8 REMARK 465 PRO A 313 REMARK 465 ALA A 314 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 9 CG SD CE REMARK 470 ASP A 10 CG OD1 OD2 REMARK 470 ASN A 39 CG OD1 ND2 REMARK 470 GLN A 94 CD OE1 NE2 REMARK 470 GLU A 106 CD OE1 OE2 REMARK 470 GLN A 132 CD OE1 NE2 REMARK 470 LYS A 207 CE NZ REMARK 470 GLU A 227 CD OE1 OE2 REMARK 470 GLU A 287 OE1 OE2 REMARK 470 ASN A 288 CG OD1 ND2 REMARK 470 ARG A 306 CZ NH1 NH2 REMARK 470 TYR A 312 C O CB CG CD1 CD2 CE1 REMARK 470 TYR A 312 CE2 CZ OH 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 O6 G B 401 O6 G B 401 2556 1.60 REMARK 500 O HOH B 754 O HOH B 754 2556 1.74 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 U B 409 O4' - C1' - N1 ANGL. DEV. = 5.6 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 SER A 206 -137.99 52.89 REMARK 500 SER A 273 -79.20 -55.77 REMARK 500 GLU A 278 -177.66 -171.35 REMARK 500 GLU A 300 4.65 -65.01 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 U B 409 0.06 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 910 DBREF 1K8W A 10 314 UNP P60340 TRUB_ECOLI 10 314 DBREF 1K8W B 401 422 PDB 1K8W 1K8W 401 422 SEQRES 1 B 22 G G C A A C G G U FHU C G A SEQRES 2 B 22 U C C C G U U G C SEQRES 1 A 327 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 327 SER GLY HIS ILE GLU GLY ARG HIS MET ASP ILE ASN GLY SEQRES 3 A 327 VAL LEU LEU LEU ASP LYS PRO GLN GLY MET SER SER ASN SEQRES 4 A 327 ASP ALA LEU GLN LYS VAL LYS ARG ILE TYR ASN ALA ASN SEQRES 5 A 327 ARG ALA GLY HIS THR GLY ALA LEU ASP PRO LEU ALA THR SEQRES 6 A 327 GLY MET LEU PRO ILE CYS LEU GLY GLU ALA THR LYS PHE SEQRES 7 A 327 SER GLN TYR LEU LEU ASP SER ASP LYS ARG TYR ARG VAL SEQRES 8 A 327 ILE ALA ARG LEU GLY GLN ARG THR ASP THR SER ASP ALA SEQRES 9 A 327 ASP GLY GLN ILE VAL GLU GLU ARG PRO VAL THR PHE SER SEQRES 10 A 327 ALA GLU GLN LEU ALA ALA ALA LEU ASP THR PHE ARG GLY SEQRES 11 A 327 ASP ILE GLU GLN ILE PRO SER MET TYR SER ALA LEU LYS SEQRES 12 A 327 TYR GLN GLY LYS LYS LEU TYR GLU TYR ALA ARG GLN GLY SEQRES 13 A 327 ILE GLU VAL PRO ARG GLU ALA ARG PRO ILE THR VAL TYR SEQRES 14 A 327 GLU LEU LEU PHE ILE ARG HIS GLU GLY ASN GLU LEU GLU SEQRES 15 A 327 LEU GLU ILE HIS CYS SER LYS GLY THR TYR ILE ARG THR SEQRES 16 A 327 ILE ILE ASP ASP LEU GLY GLU LYS LEU GLY CYS GLY ALA SEQRES 17 A 327 HIS VAL ILE TYR LEU ARG ARG LEU ALA VAL SER LYS TYR SEQRES 18 A 327 PRO VAL GLU ARG MET VAL THR LEU GLU HIS LEU ARG GLU SEQRES 19 A 327 LEU VAL GLU GLN ALA GLU GLN GLN ASP ILE PRO ALA ALA SEQRES 20 A 327 GLU LEU LEU ASP PRO LEU LEU MET PRO MET ASP SER PRO SEQRES 21 A 327 ALA SER ASP TYR PRO VAL VAL ASN LEU PRO LEU THR SER SEQRES 22 A 327 SER VAL TYR PHE LYS ASN GLY ASN PRO VAL ARG THR SER SEQRES 23 A 327 GLY ALA PRO LEU GLU GLY LEU VAL ARG VAL THR GLU GLY SEQRES 24 A 327 GLU ASN GLY LYS PHE ILE GLY MET GLY GLU ILE ASP ASP SEQRES 25 A 327 GLU GLY ARG VAL ALA PRO ARG ARG LEU VAL VAL GLU TYR SEQRES 26 A 327 PRO ALA MODRES 1K8W FHU B 410 U HET FHU B 410 22 HET SO4 B 907 5 HET SO4 A 901 5 HET SO4 A 902 5 HET SO4 A 903 5 HET SO4 A 904 5 HET SO4 A 905 5 HET SO4 A 906 5 HET SO4 A 908 5 HET SO4 A 909 5 HET SO4 A 910 5 HETNAM FHU (5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5'- HETNAM 2 FHU MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 1 FHU C9 H14 F N2 O10 P FORMUL 3 SO4 10(O4 S 2-) FORMUL 13 HOH *259(H2 O) 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 LEU A 136 GLN A 142 1 7 HELIX 6 6 TYR A 179 LEU A 191 1 13 HELIX 7 7 PRO A 209 MET A 213 5 5 HELIX 8 8 LEU A 216 GLN A 229 1 14 HELIX 9 9 ALA A 233 ASP A 238 1 6 HELIX 10 10 PRO A 239 LEU A 241 5 3 HELIX 11 11 ASP A 245 SER A 249 5 5 HELIX 12 12 PRO A 257 LYS A 265 1 9 SHEET 1 A 8 GLY A 117 GLN A 121 0 SHEET 2 A 8 ARG A 151 GLU A 164 -1 O ARG A 151 N GLN A 121 SHEET 3 A 8 GLU A 167 CYS A 174 -1 O GLU A 171 N LEU A 159 SHEET 4 A 8 LYS A 74 LEU A 82 -1 N ALA A 80 O LEU A 168 SHEET 5 A 8 ALA A 195 VAL A 205 -1 O HIS A 196 N ARG A 81 SHEET 6 A 8 THR A 52 LEU A 59 1 N THR A 52 O ARG A 202 SHEET 7 A 8 GLY A 13 LYS A 19 -1 N GLY A 13 O LEU A 59 SHEET 8 A 8 VAL A 214 THR A 215 1 O VAL A 214 N ASP A 18 SHEET 1 B 7 GLY A 117 GLN A 121 0 SHEET 2 B 7 ARG A 151 GLU A 164 -1 O ARG A 151 N GLN A 121 SHEET 3 B 7 GLU A 167 CYS A 174 -1 O GLU A 171 N LEU A 159 SHEET 4 B 7 LYS A 74 LEU A 82 -1 N ALA A 80 O LEU A 168 SHEET 5 B 7 ALA A 195 VAL A 205 -1 O HIS A 196 N ARG A 81 SHEET 6 B 7 THR A 52 LEU A 59 1 N THR A 52 O ARG A 202 SHEET 7 B 7 ALA A 41 HIS A 43 -1 N GLY A 42 O CYS A 58 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 2 LYS A 130 TYR A 131 0 SHEET 2 D 2 LYS A 134 LYS A 135 -1 O LYS A 134 N TYR A 131 SHEET 1 E 4 VAL A 253 LEU A 256 0 SHEET 2 E 4 LEU A 280 GLU A 285 1 O ARG A 282 N VAL A 254 SHEET 3 E 4 LYS A 290 ILE A 297 -1 O GLY A 295 N VAL A 281 SHEET 4 E 4 VAL A 303 LEU A 308 -1 O ARG A 307 N MET A 294 LINK O3' U B 409 P FHU B 410 1555 1555 1.60 LINK O3' FHU B 410 P C B 411 1555 1555 1.60 SITE 1 AC1 5 LYS A 31 ARG A 34 ARG A 220 HOH A 562 SITE 2 AC1 5 SO4 A 902 SITE 1 AC2 3 LYS A 31 ARG A 220 SO4 A 901 SITE 1 AC3 3 PRO A 257 THR A 272 SER A 273 SITE 1 AC4 3 ARG A 81 HOH A 652 HOH A 679 SITE 1 AC5 3 ARG A 271 ARG A 302 HOH A 680 SITE 1 AC6 4 THR A 102 GLN A 132 GLY A 192 C B 406 SITE 1 AC7 3 PRO A 49 ASP A 113 G B 412 SITE 1 AC8 6 ARG A 77 TYR A 199 LEU A 203 GLN A 225 SITE 2 AC8 6 GLN A 228 GLN A 229 SITE 1 AC9 6 ARG A 85 GLU A 97 LYS A 134 GLU A 138 SITE 2 AC9 6 GLN A 142 HOH A 742 SITE 1 BC1 5 LEU A 258 SER A 261 VAL A 262 LYS A 265 SITE 2 BC1 5 GLU A 285 CRYST1 145.054 40.361 77.987 90.00 110.60 90.00 C 1 2 1 4 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 0.006894 0.000000 0.002591 0.00000 SCALE2 0.000000 0.024776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013699 0.00000