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- PDB-7cfy: Crystal Structure of YbeA CP74 W48F -

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Basic information

Entry
Database: PDB / ID: 7cfy
TitleCrystal Structure of YbeA CP74 W48F
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: 2.4051 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 W48F
Authors: Liu, C.Y. / Lai, C.H. / Hsu, S.T.D. / Lyu, P.C.
History
DepositionJun 29, 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
C: Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H
D: Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H


Theoretical massNumber of molelcules
Total (without water)70,4064
Polymers70,4064
Non-polymers00
Water72140
1
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-56 kcal/mol
Surface area15050 Å2
MethodPISA
2
C: Ribosomal RNA large subunit methyltransferase H,Ribosomal RNA large subunit methyltransferase H
D: 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-63 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.137, 57.833, 69.629
Angle α, β, γ (deg.)67.170, 90.050, 90.150
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: 17601.387 Da / Num. of mol.: 4 / Mutation: W120F
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.: 40 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Sodium acetate pH 4.5, 0.1M Calcium acetate hydrate, 10% 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 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.4051→30 Å / Num. obs: 20734 / % possible obs: 95.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.072 / Rrim(I) all: 0.122 / Χ2: 1.002 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.41-2.52.40.48819940.7760.3560.6071.01390.1
2.5-2.62.70.44320350.8490.3170.5471.01894.9
2.6-2.712.90.38420670.8970.2690.4711.02196.7
2.71-2.862.90.29221170.9420.2080.361.00696.8
2.86-3.042.90.20521290.9570.1450.2520.99296.9
3.04-3.272.90.15520870.9730.110.1910.98696.9
3.27-3.62.80.09820680.9860.0710.1211.02196.2
3.6-4.122.70.06920710.9920.050.0860.9895.8
4.12-5.182.60.05320400.9940.0390.0660.98194.2
5.18-23.72252.40.03721260.9960.0330.050.99897.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.41 Å23.72 Å
Translation2.41 Å23.72 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: 2.4051→23.7225 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 34.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3067 2004 9.68 %
Rwork0.2175 18709 -
obs0.226 20713 94.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.5 Å2 / Biso mean: 42.2506 Å2 / Biso min: 16.35 Å2
Refinement stepCycle: final / Resolution: 2.4051→23.7225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4425 0 0 40 4465
Biso mean---36.87 -
Num. residues----587
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4051-2.46520.32651240.2466108878
2.4652-2.53180.30951430.2477132094
2.5318-2.60620.34371480.2399135996
2.6062-2.69020.33061380.2539135597
2.6902-2.78620.38041440.2523140797
2.7862-2.89760.33031410.246133397
2.8976-3.02920.36081490.2466136597
3.0292-3.18860.36831390.2467137297
3.1886-3.38780.33111470.2559135296
3.3878-3.64850.31881510.2212135596
3.6485-4.01410.33121490.2038133996
4.0141-4.59130.25071400.1909131293
4.5913-5.77080.28081480.1975139797
5.7708-23.72250.24531430.1794135597

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