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- PDB-7cf7: Crystal Structure of YbeA CP74 W72F -

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Basic information

Entry
Database: PDB / ID: 7cf7
TitleCrystal Structure of YbeA CP74 W72F
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: 1.6178 Å
AuthorsLiu, 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 W72F
Authors: Liu, C.Y. / Lai, C.H. / Hsu, S.T.D. / Lyu, P.C.
History
DepositionJun 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 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
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-65 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.628, 38.698, 52.325
Angle α, β, γ (deg.)75.290, 73.800, 76.470
Int Tables number1
Space group name H-MP1

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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: W144F
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.: 265 / 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: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Sodium cacodylate pH 6.5, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.6178→30 Å / Num. obs: 32081 / % possible obs: 93.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.042 / Rrim(I) all: 0.069 / Χ2: 1.021 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.682.40.38531440.8320.2980.4891.02692.7
1.68-1.752.70.36831990.8550.2650.4551.02393.7
1.75-1.822.90.27632200.9230.1910.3371.0494.2
1.82-1.922.90.18432400.9580.1270.2241.02194.9
1.92-2.042.90.12832670.980.090.1571.02894.5
2.04-2.22.80.0932130.9870.0650.1111.0494.5
2.2-2.422.70.06632340.9920.0480.0821.00994.6
2.42-2.772.70.05432230.9940.0390.0671.00294.2
2.77-3.492.60.03931220.9960.030.051.00491.2
3.49-302.20.02532190.9970.0240.0351.00694.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.62 Å23.61 Å
Translation1.62 Å23.61 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.3phasing
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZYO

5zyo


Resolution: 1.6178→23.6084 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1985 6.19 %
Rwork0.1885 30094 -
obs0.1904 32079 93.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.21 Å2 / Biso mean: 24.4798 Å2 / Biso min: 9.35 Å2
Refinement stepCycle: final / Resolution: 1.6178→23.6084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 0 265 2494
Biso mean---31.13 -
Num. residues----291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6178-1.65820.28011290.2361185783
1.6582-1.7030.26941280.2204220194
1.703-1.75310.27541560.2181216494
1.7531-1.80970.24961390.2016217794
1.8097-1.87440.22351440.1975218395
1.8744-1.94940.22381410.1982218895
1.9494-2.03810.23321480.1849216195
2.0381-2.14540.2061450.1802219194
2.1454-2.27980.23021450.1834218895
2.2798-2.45560.22471410.1951217594
2.4556-2.70240.22931460.2032216494
2.7024-3.09270.24781400.2036215693
3.0927-3.89360.20691350.1772211491
3.8936-23.60840.17871480.1689217595

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