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- PDB-7cem: Crystal Structure of YbeA CP74 W7F -

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Basic information

Entry
Database: PDB / ID: 7cem
TitleCrystal Structure of YbeA CP74 W7F
ComponentsRibosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H
KeywordsTRANSFERASE / YbeA
Function / homology
Function and homology information


23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / rRNA base methylation / rRNA methylation / ribosome binding / protein homodimerization activity / cytoplasm
Similarity search - Function
RNA methyltransferase RlmH / Predicted SPOUT methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
Ribosomal RNA large subunit methyltransferase H
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4251 Å
AuthorsLiu, C.Y. / Wu, C.Y. / Lai, C.H. / Hsu, S.T.D. / Lyu, P.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal Structure of YbeA CP74 W7F
Authors: Liu, C.Y. / Wu, C.Y. / Lai, C.H. / Hsu, S.T.D. / Lyu, P.C.
History
DepositionJun 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H
B: Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H


Theoretical massNumber of molelcules
Total (without water)35,2032
Polymers35,2032
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-68 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.784, 128.784, 115.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

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Components

#1: Protein Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H / 23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA ...23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase RlmH


Mass: 17601.389 Da / Num. of mol.: 2 / Mutation: W79F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: rlmH, ybeA, b0636, JW0631 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A8I8, 23S rRNA (pseudouridine1915-N3)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.0M Ammonium sulfate 0.1M Sodium HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2019
Diffraction measurementDetails: 1.00 degrees, 10.0 sec, detector distance 230.00 mm
Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.142 / Number: 256316
ReflectionResolution: 2.425→30 Å / Num. obs: 18788 / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.04 / Rrim(I) all: 0.148 / Χ2: 1.052 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.43-2.52110.83618550.7630.2640.8781.09999.8
2.52-2.62130.69418310.8970.20.7231.083100
2.62-2.7413.90.58318550.9390.1610.6051.081100
2.74-2.8814.20.43918390.9650.120.4551.079100
2.88-3.0614.40.29918630.980.0810.311.081100
3.06-3.314.40.21118620.9910.0570.2181.054100
3.3-3.6314.30.11818830.9970.0320.1220.992100
3.63-4.1514.30.07718910.9980.0210.081.03100
4.15-5.23140.05618960.9990.0160.0590.999100
5.23-3012.80.05620130.9990.0160.0591.034100
Cell measurementReflection used: 256316

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZYO

5zyo


Resolution: 2.4251→28.9931 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 1879 10 %
Rwork0.2172 16906 -
obs0.2228 18785 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.11 Å2 / Biso mean: 39.3724 Å2 / Biso min: 15.78 Å2
Refinement stepCycle: final / Resolution: 2.4251→28.9931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 0 75 2442
Biso mean---35.13 -
Num. residues----312
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4251-2.49060.31581410.26021272
2.4906-2.56390.32171420.24351281
2.5639-2.64660.31591420.23551279
2.6466-2.74110.29121420.23441279
2.7411-2.85080.27431450.23451290
2.8508-2.98040.28221420.22811280
2.9804-3.13730.30591430.2511286
3.1373-3.33360.30271430.24011289
3.3336-3.59060.32511440.2181297
3.5906-3.95110.25921450.2071298
3.9511-4.5210.21181450.17371315
4.521-5.68890.23351480.20071335
5.6889-28.99310.26841570.21691405

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