HEADER ISOMERASE 18-OCT-06 2IST TITLE CRYSTAL STRUCTURE OF RLUD FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RRNA- URIDINE ISOMERASE D, RRNA PSEUDOURIDYLATE SYNTHASE D; COMPND 5 EC: 5.4.99.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: RLUD, SFHB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)(PLYSS); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS ALPHA-BETA FOLD, S4 DOMAIN, PSEUDOURIDINE SYNTHASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.G.FOSTER,J.S.FINER-MOORE,R.M.STROUD REVDAT 4 21-FEB-24 2IST 1 REMARK REVDAT 3 13-JUL-11 2IST 1 VERSN REVDAT 2 24-FEB-09 2IST 1 VERSN REVDAT 1 31-OCT-06 2IST 0 JRNL AUTH P.G.FOSTER,J.S.FINER-MOORE,R.M.STROUD JRNL TITL CRYSTAL STRUCTURE OF RLUD FROM E. COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 36440 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 + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3638 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2141 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.3430 REMARK 3 BIN FREE R VALUE SET COUNT : 231 REMARK 3 BIN FREE R VALUE : 0.3850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2568 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 251 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 0.58000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.782 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2646 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3591 ; 1.625 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 321 ; 6.298 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;33.489 ;22.756 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 458 ;14.856 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.880 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 398 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2030 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1205 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1747 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 225 ; 0.182 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 36 ; 0.196 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.104 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1684 ; 1.108 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2632 ; 1.699 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1080 ; 2.712 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 959 ; 4.142 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 72 REMARK 3 ORIGIN FOR THE GROUP (A): 30.2920 59.6490 -24.3390 REMARK 3 T TENSOR REMARK 3 T11: -0.1359 T22: -0.0478 REMARK 3 T33: -0.0026 T12: -0.0687 REMARK 3 T13: 0.0601 T23: -0.0579 REMARK 3 L TENSOR REMARK 3 L11: 6.3537 L22: 7.7654 REMARK 3 L33: 3.4139 L12: 5.1865 REMARK 3 L13: 1.0211 L23: 2.1974 REMARK 3 S TENSOR REMARK 3 S11: 0.1266 S12: -0.0813 S13: 0.2107 REMARK 3 S21: 0.1169 S22: 0.1195 S23: 0.1900 REMARK 3 S31: -0.0996 S32: 0.2556 S33: -0.2461 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 77 A 155 REMARK 3 ORIGIN FOR THE GROUP (A): 33.2960 54.3580 13.9830 REMARK 3 T TENSOR REMARK 3 T11: -0.0379 T22: -0.0085 REMARK 3 T33: -0.0129 T12: -0.0171 REMARK 3 T13: -0.0048 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 1.3624 L22: 2.4943 REMARK 3 L33: 0.4900 L12: 1.2226 REMARK 3 L13: -0.3422 L23: -0.3226 REMARK 3 S TENSOR REMARK 3 S11: -0.1823 S12: 0.1130 S13: -0.0102 REMARK 3 S21: -0.2127 S22: 0.1566 S23: -0.0665 REMARK 3 S31: -0.0287 S32: -0.0809 S33: 0.0258 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2IST COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039971. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 103; 103 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRL; SSRL REMARK 200 BEAMLINE : BL7-1; BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : NULL; NULL REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL; NULL REMARK 200 DETECTOR MANUFACTURER : NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36440 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 53.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD COMBINED WITH MIR 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 (%): 57.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: EQUAL PARTS PROTEIN (~3MG/ML) AND REMARK 280 PRECIPITANT 12-18% PEG 4000, 100 MM TRIS, PH 8.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 33.66000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.90000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.57000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.90000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.66000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.57000 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 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 GLU A 73 REMARK 465 GLU A 74 REMARK 465 ALA A 75 REMARK 465 LEU A 326 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 ASP A 324 CG OD1 OD2 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 O2 BCT A 804 O HOH A 489 1.96 REMARK 500 NE2 GLN A 303 O HOH A 537 2.09 REMARK 500 O HOH A 328 O HOH A 598 2.12 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 ARG A 213 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ILE A 71 -114.63 -112.11 REMARK 500 ASP A 81 78.84 -66.39 REMARK 500 ASP A 90 -156.11 -131.89 REMARK 500 LYS A 320 20.63 -72.97 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 CL A 477 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BCT A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BCT A 804 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QYU RELATED DB: PDB REMARK 900 STRUCTURE OF THE CATALYTIC DOMAIN OF 23S RRNA PSEUDOURIDINE REMARK 900 SYNTHASE RLUD REMARK 900 RELATED ID: 1PRZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PSEUDOURIDINE SYNTHASE RLUD CATALYTIC MODULE REMARK 900 RELATED ID: 1V9F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF PSEUDOURIDINE SYNTHASE REMARK 900 RLUD FROM ESCHERICHIA COLI DBREF 2IST A 2 326 UNP P33643 RLUD_ECOLI 1 325 SEQRES 1 A 325 ALA GLN ARG VAL GLN LEU THR ALA THR VAL SER GLU ASN SEQRES 2 A 325 GLN LEU GLY GLN ARG LEU ASP GLN ALA LEU ALA GLU MET SEQRES 3 A 325 PHE PRO ASP TYR SER ARG SER ARG ILE LYS GLU TRP ILE SEQRES 4 A 325 LEU ASP GLN ARG VAL LEU VAL ASN GLY LYS VAL CYS ASP SEQRES 5 A 325 LYS PRO LYS GLU LYS VAL LEU GLY GLY GLU GLN VAL ALA SEQRES 6 A 325 ILE ASN ALA GLU ILE GLU GLU GLU ALA ARG PHE GLU PRO SEQRES 7 A 325 GLN ASP ILE PRO LEU ASP ILE VAL TYR GLU ASP GLU ASP SEQRES 8 A 325 ILE ILE ILE ILE ASN LYS PRO ARG ASP LEU VAL VAL HIS SEQRES 9 A 325 PRO GLY ALA GLY ASN PRO ASP GLY THR VAL LEU ASN ALA SEQRES 10 A 325 LEU LEU HIS TYR TYR PRO PRO ILE ALA ASP VAL PRO ARG SEQRES 11 A 325 ALA GLY ILE VAL HIS ARG LEU ASP LYS ASP THR THR GLY SEQRES 12 A 325 LEU MET VAL VAL ALA LYS THR VAL PRO ALA GLN THR ARG SEQRES 13 A 325 LEU VAL GLU SER LEU GLN ARG ARG GLU ILE THR ARG GLU SEQRES 14 A 325 TYR GLU ALA VAL ALA ILE GLY HIS MET THR ALA GLY GLY SEQRES 15 A 325 THR VAL ASP GLU PRO ILE SER ARG HIS PRO THR LYS ARG SEQRES 16 A 325 THR HIS MET ALA VAL HIS PRO MET GLY LYS PRO ALA VAL SEQRES 17 A 325 THR HIS TYR ARG ILE MET GLU HIS PHE ARG VAL HIS THR SEQRES 18 A 325 ARG LEU ARG LEU ARG LEU GLU THR GLY ARG THR HIS GLN SEQRES 19 A 325 ILE ARG VAL HIS MET ALA HIS ILE THR HIS PRO LEU VAL SEQRES 20 A 325 GLY ASP PRO VAL TYR GLY GLY ARG PRO ARG PRO PRO LYS SEQRES 21 A 325 GLY ALA SER GLU ALA PHE ILE SER THR LEU ARG LYS PHE SEQRES 22 A 325 ASP ARG GLN ALA LEU HIS ALA THR MET LEU ARG LEU TYR SEQRES 23 A 325 HIS PRO ILE SER GLY ILE GLU MET GLU TRP HIS ALA PRO SEQRES 24 A 325 ILE PRO GLN ASP MET VAL GLU LEU ILE GLU VAL MET ARG SEQRES 25 A 325 ALA ASP PHE GLU GLU HIS LYS ASP GLU VAL ASP TRP LEU HET CL A 477 1 HET BCT A 803 4 HET BCT A 804 4 HETNAM CL CHLORIDE ION HETNAM BCT BICARBONATE ION FORMUL 2 CL CL 1- FORMUL 3 BCT 2(C H O3 1-) FORMUL 5 HOH *251(H2 O) HELIX 1 1 SER A 12 LEU A 16 5 5 HELIX 2 2 ARG A 19 PHE A 28 1 10 HELIX 3 3 SER A 32 ASP A 42 1 11 HELIX 4 4 THR A 114 TYR A 123 1 10 HELIX 5 5 PRO A 124 ILE A 134 5 11 HELIX 6 6 THR A 151 ARG A 164 1 14 HELIX 7 7 HIS A 234 ILE A 243 1 10 HELIX 8 8 SER A 264 PHE A 274 1 11 HELIX 9 9 PRO A 302 HIS A 319 1 18 SHEET 1 A 4 ARG A 4 THR A 10 0 SHEET 2 A 4 GLN A 64 GLU A 70 -1 O ALA A 69 N VAL A 5 SHEET 3 A 4 VAL A 45 VAL A 47 -1 N LEU A 46 O ALA A 66 SHEET 4 A 4 LYS A 50 VAL A 51 -1 O LYS A 50 N VAL A 47 SHEET 1 B 8 ILE A 86 GLU A 89 0 SHEET 2 B 8 ILE A 93 LYS A 98 -1 O ILE A 95 N TYR A 88 SHEET 3 B 8 THR A 143 ALA A 149 -1 O GLY A 144 N LYS A 98 SHEET 4 B 8 LEU A 279 TYR A 287 1 O ALA A 281 N THR A 143 SHEET 5 B 8 THR A 168 ILE A 176 -1 N THR A 168 O ARG A 285 SHEET 6 B 8 HIS A 221 LEU A 228 -1 O LEU A 224 N ALA A 173 SHEET 7 B 8 VAL A 209 HIS A 217 -1 N GLU A 216 O ARG A 223 SHEET 8 B 8 GLY A 183 ASP A 186 -1 N VAL A 185 O THR A 210 SHEET 1 C 5 ILE A 86 GLU A 89 0 SHEET 2 C 5 ILE A 93 LYS A 98 -1 O ILE A 95 N TYR A 88 SHEET 3 C 5 THR A 143 ALA A 149 -1 O GLY A 144 N LYS A 98 SHEET 4 C 5 LEU A 279 TYR A 287 1 O ALA A 281 N THR A 143 SHEET 5 C 5 GLU A 294 HIS A 298 -1 O MET A 295 N LEU A 286 SHEET 1 D 2 ILE A 189 ARG A 191 0 SHEET 2 D 2 MET A 199 VAL A 201 -1 O ALA A 200 N SER A 190 SITE 1 AC1 2 ASP A 139 TYR A 171 SITE 1 AC2 4 GLU A 310 ARG A 313 HOH A 509 HOH A 528 SITE 1 AC3 3 PRO A 83 LEU A 84 HOH A 489 CRYST1 67.320 75.140 85.800 90.00 90.00 90.00 P 21 21 21 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 0.014854 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011655 0.00000