HEADER LYASE 13-JAN-02 1KSK TITLE STRUCTURE OF RSUA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 16S PSEUDOURIDYLATE 516 SYNTHASE, 16S PSEUDOURIDINE 516 COMPND 5 SYNTHASE, URACIL HYDROLYASE; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: DL41 KEYWDS PSEUDOURIDINE SYNTHASE, RSUA, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.SIVARAMAN,V.SAUVE,R.LAROCQUE,E.A.STURA,J.D.SCHRAG,M.CYGLER,A.MATTE REVDAT 6 31-JAN-18 1KSK 1 REMARK REVDAT 5 11-OCT-17 1KSK 1 REMARK REVDAT 4 24-FEB-09 1KSK 1 VERSN REVDAT 3 19-JUN-02 1KSK 1 JRNL REVDAT 2 01-MAY-02 1KSK 1 SEQADV REVDAT 1 24-APR-02 1KSK 0 JRNL AUTH J.SIVARAMAN,V.SAUVE,R.LAROCQUE,E.A.STURA,J.D.SCHRAG, JRNL AUTH 2 M.CYGLER,A.MATTE JRNL TITL STRUCTURE OF THE 16S RRNA PSEUDOURIDINE SYNTHASE RSUA BOUND JRNL TITL 2 TO URACIL AND UMP. JRNL REF NAT.STRUCT.BIOL. V. 9 353 2002 JRNL REFN ISSN 1072-8368 JRNL PMID 11953756 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 30730 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) : 0.217 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2089 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 : 1828 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 222 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.25 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 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 1KSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968634 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADX REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31168 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23500 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: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MALATE, KSCN, ISOPROPONAL, REMARK 280 GLYCEROL, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 18K, REMARK 280 TEMPERATURE 291.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 24.38550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.38550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.61000 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: 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 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 ALA A 48 CB REMARK 470 ALA A 55 CB REMARK 470 GLN A 57 CB CG CD OE1 NE2 REMARK 470 GLU A 157 CG CD OE1 OE2 REMARK 470 VAL A 230 CG1 CG2 REMARK 470 VAL A 231 CG1 CG2 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 88 75.22 -117.39 REMARK 500 VAL A 91 45.62 37.35 REMARK 500 LYS A 158 -72.53 -74.61 REMARK 500 ASN A 195 -166.67 -115.86 REMARK 500 SER A 229 15.24 -141.39 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 URA A 232 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KSL RELATED DB: PDB REMARK 900 STRUCTURE OF RSUA REMARK 900 RELATED ID: 1KSV RELATED DB: PDB REMARK 900 STRUCTURE OF RSUA DBREF 1KSK A 1 231 UNP P0AA43 RSUA_ECOLI 1 231 SEQADV 1KSK GLY A 1A UNP P0AA43 CLONING ARTIFACT SEQADV 1KSK SER A 1B UNP P0AA43 CLONING ARTIFACT SEQADV 1KSK HIS A 1C UNP P0AA43 CLONING ARTIFACT SEQADV 1KSK MSE A 1 UNP P0AA43 MET 1 MODIFIED RESIDUE SEQADV 1KSK MSE A 64 UNP P0AA43 MET 64 MODIFIED RESIDUE SEQADV 1KSK MSE A 111 UNP P0AA43 MET 111 MODIFIED RESIDUE SEQADV 1KSK MSE A 189 UNP P0AA43 MET 189 MODIFIED RESIDUE SEQRES 1 A 234 GLY SER HIS MSE ARG LEU ASP LYS PHE ILE ALA GLN GLN SEQRES 2 A 234 LEU GLY VAL SER ARG ALA ILE ALA GLY ARG GLU ILE ARG SEQRES 3 A 234 GLY ASN ARG VAL THR VAL ASP GLY GLU ILE VAL ARG ASN SEQRES 4 A 234 ALA ALA PHE LYS LEU LEU PRO GLU HIS ASP VAL ALA TYR SEQRES 5 A 234 ASP GLY ASN PRO LEU ALA GLN GLN HIS GLY PRO ARG TYR SEQRES 6 A 234 PHE MSE LEU ASN LYS PRO GLN GLY TYR VAL CYS SER THR SEQRES 7 A 234 ASP ASP PRO ASP HIS PRO THR VAL LEU TYR PHE LEU ASP SEQRES 8 A 234 GLU PRO VAL ALA TRP LYS LEU HIS ALA ALA GLY ARG LEU SEQRES 9 A 234 ASP ILE ASP THR THR GLY LEU VAL LEU MSE THR ASP ASP SEQRES 10 A 234 GLY GLN TRP SER HIS ARG ILE THR SER PRO ARG HIS HIS SEQRES 11 A 234 CYS GLU LYS THR TYR LEU VAL THR LEU GLU SER PRO VAL SEQRES 12 A 234 ALA ASP ASP THR ALA GLU GLN PHE ALA LYS GLY VAL GLN SEQRES 13 A 234 LEU HIS ASN GLU LYS ASP LEU THR LYS PRO ALA VAL LEU SEQRES 14 A 234 GLU VAL ILE THR PRO THR GLN VAL ARG LEU THR ILE SER SEQRES 15 A 234 GLU GLY ARG TYR HIS GLN VAL LYS ARG MSE PHE ALA ALA SEQRES 16 A 234 VAL GLY ASN HIS VAL VAL GLU LEU HIS ARG GLU ARG ILE SEQRES 17 A 234 GLY GLY ILE THR LEU ASP ALA ASP LEU ALA PRO GLY GLU SEQRES 18 A 234 TYR ARG PRO LEU THR GLU GLU GLU ILE ALA SER VAL VAL MODRES 1KSK MSE A 1 MET SELENOMETHIONINE MODRES 1KSK MSE A 64 MET SELENOMETHIONINE MODRES 1KSK MSE A 111 MET SELENOMETHIONINE MODRES 1KSK MSE A 189 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 64 8 HET MSE A 111 8 HET MSE A 189 8 HET URA A 232 8 HETNAM MSE SELENOMETHIONINE HETNAM URA URACIL FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 URA C4 H4 N2 O2 FORMUL 3 HOH *222(H2 O) HELIX 1 1 LEU A 3 GLY A 12 1 10 HELIX 2 2 SER A 14 GLY A 24 1 11 HELIX 3 3 THR A 82 LEU A 87 5 6 HELIX 4 4 VAL A 91 LEU A 95 5 5 HELIX 5 5 ASP A 114 SER A 123 1 10 HELIX 6 6 ASP A 143 GLY A 151 1 9 HELIX 7 7 HIS A 184 VAL A 193 1 10 HELIX 8 8 THR A 223 ALA A 228 1 6 SHEET 1 A 2 MSE A 1 ARG A 2 0 SHEET 2 A 2 LYS A 40 LEU A 41 -1 N LEU A 41 O MSE A 1 SHEET 1 B 4 GLU A 32 ILE A 33 0 SHEET 2 B 4 VAL A 47 TYR A 49 -1 SHEET 3 B 4 ASN A 52 LEU A 54 -1 O ASN A 52 N TYR A 49 SHEET 1 C11 TYR A 219 PRO A 221 0 SHEET 2 C11 TYR A 62 LYS A 67 -1 N MSE A 64 O ARG A 220 SHEET 3 C11 THR A 106 THR A 112 -1 O GLY A 107 N LYS A 67 SHEET 4 C11 HIS A 96 ALA A 97 -1 N HIS A 96 O THR A 112 SHEET 5 C11 THR A 106 THR A 112 -1 O THR A 112 N HIS A 96 SHEET 6 C11 VAL A 197 ILE A 205 1 O LEU A 200 N THR A 106 SHEET 7 C11 ILE A 208 THR A 209 -1 N ILE A 208 O ILE A 205 SHEET 8 C11 VAL A 197 ILE A 205 -1 N ILE A 205 O ILE A 208 SHEET 9 C11 LYS A 130 LEU A 136 -1 O THR A 131 N GLU A 203 SHEET 10 C11 GLN A 173 ILE A 178 -1 O VAL A 174 N VAL A 134 SHEET 11 C11 VAL A 165 THR A 170 -1 O VAL A 165 N THR A 177 LINK C HIS A 1C N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N ARG A 2 1555 1555 1.33 LINK C PHE A 63 N MSE A 64 1555 1555 1.33 LINK C MSE A 64 N LEU A 65 1555 1555 1.33 LINK C LEU A 110 N MSE A 111 1555 1555 1.33 LINK C MSE A 111 N THR A 112 1555 1555 1.33 LINK C ARG A 188 N MSE A 189 1555 1555 1.33 LINK C MSE A 189 N PHE A 190 1555 1555 1.33 SITE 1 AC1 6 ASP A 102 THR A 105 TYR A 132 HIS A 184 SITE 2 AC1 6 GLN A 185 VAL A 186 CRYST1 48.771 149.220 35.200 90.00 90.00 90.00 P 21 21 2 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 0.020504 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006702 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028409 0.00000