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- PDB-1v9k: The crystal structure of the catalytic domain of pseudouridine sy... -

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Basic information

Entry
Database: PDB / ID: 1v9k
TitleThe crystal structure of the catalytic domain of pseudouridine synthase RluC from Escherichia coli
ComponentsRibosomal large subunit pseudouridine synthase C
KeywordsLYASE / pseudouridine syntase / RNA binding
Function / homology
Function and homology information


23S rRNA pseudouridine955/2504/2580 synthase / 23S rRNA pseudouridine(955/2504/2580) synthase activity / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding / cytosol
Similarity search - Function
Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / : / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / S4 RNA-binding domain profile. ...Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / : / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal large subunit pseudouridine synthase C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMachida, Y. / Mizutani, K. / Unzai, S. / Park, S.-Y. / Tame, J.R.H.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli
Authors: Mizutani, K. / Machida, Y. / Unzai, S. / Park, S.-Y. / Tame, J.R.H.
History
DepositionJan 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal large subunit pseudouridine synthase C
B: Ribosomal large subunit pseudouridine synthase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2444
Polymers52,0522
Non-polymers1922
Water3,081171
1
A: Ribosomal large subunit pseudouridine synthase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1222
Polymers26,0261
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal large subunit pseudouridine synthase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1222
Polymers26,0261
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.725, 96.725, 86.884
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ribosomal large subunit pseudouridine synthase C / Pseudouridylate synthase / Uracil hydrolyase


Mass: 26026.105 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN / Mutation: L96M/L315M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RLUC / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AA39, pseudouridylate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, HEPES, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97876, 0.97919, 0.98140
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2003
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978761
20.979191
30.98141
ReflectionResolution: 2→20 Å / Num. obs: 35502 / % possible obs: 98 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 2→2.07 Å / % possible all: 83.5

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 4.669 / SU ML: 0.133 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.219 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27551 1583 5.1 %RANDOM
Rwork0.20917 ---
obs0.21254 35502 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.263 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0.56 Å20 Å2
2---1.11 Å20 Å2
3---1.67 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 10 171 3795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0213686
X-RAY DIFFRACTIONr_angle_refined_deg2.081.964956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685452
X-RAY DIFFRACTIONr_chiral_restr0.1820.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022788
X-RAY DIFFRACTIONr_nbd_refined0.2270.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2208
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.218
X-RAY DIFFRACTIONr_mcbond_it1.2421.52248
X-RAY DIFFRACTIONr_mcangle_it2.15123600
X-RAY DIFFRACTIONr_scbond_it3.79631438
X-RAY DIFFRACTIONr_scangle_it5.6994.51356
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.316 82
Rwork0.221 1741
obs-1823

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