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- PDB-4dcm: Crystal Structure of methyltransferase RlmG modifying G1835 of 23... -

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Basic information

Entry
Database: PDB / ID: 4dcm
TitleCrystal Structure of methyltransferase RlmG modifying G1835 of 23S rRNA in Escherichia coli
ComponentsRibosomal RNA large subunit methyltransferase G
KeywordsTRANSFERASE / 23S rRNA (guanine1835-N2)-methyltransferase
Function / homology
Function and homology information


23S rRNA (guanine1835-N2)-methyltransferase / 23S rRNA (guanine(1835)-N(2))-methyltransferase activity / rRNA (guanine-N2-)-methyltransferase activity / rRNA base methylation / nucleic acid binding / cytoplasm
Similarity search - Function
rRNA (guanine-N2-)-methyltransferase, RsmD / : / Methyltransferase small domain / Methyltransferase small domain / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / Ribosomal RNA large subunit methyltransferase G
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.297 Å
AuthorsZhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Rna / Year: 2012
Title: Structural insights into the function of 23S rRNA methyltransferase RlmG (m2G1835) from Escherichia coli.
Authors: Zhang, H. / Gao, Z.Q. / Wei, Y. / Wang, W.J. / Liu, G.F. / Shtykova, E.V. / Xu, J.H. / Dong, Y.H.
History
DepositionJan 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA large subunit methyltransferase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0714
Polymers42,4601
Non-polymers6113
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.185, 42.134, 72.429
Angle α, β, γ (deg.)90.00, 104.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal RNA large subunit methyltransferase G / 23S rRNA m2G1835 methyltransferase / rRNA (guanine-N(2)-)-methyltransferase RlmG


Mass: 42460.395 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 9-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b3084, JW5513, rlmG, ygjO / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P42596, 23S rRNA (guanine1835-N2)-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Tris pH7.5, 5% (w/v) PEG 8000, 1% (w/v) protamine sulfate, 0.02M HEPES sodium pH6.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.297→50 Å / Num. all: 17821 / Num. obs: 16968 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 39.71
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 5.62 / Num. unique all: 914 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.297→29.984 Å / SU ML: 0.65 / σ(F): 1.34 / Phase error: 25.46 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 1715 5.08 %RANDOM
Rwork0.2007 ---
all0.2033 ---
obs0.2033 16968 98.3 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.475 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8205 Å20 Å21.3275 Å2
2--6.5228 Å20 Å2
3----2.7022 Å2
Refinement stepCycle: LAST / Resolution: 2.297→29.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 41 128 2999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062928
X-RAY DIFFRACTIONf_angle_d0.9783974
X-RAY DIFFRACTIONf_dihedral_angle_d16.6451083
X-RAY DIFFRACTIONf_chiral_restr0.061459
X-RAY DIFFRACTIONf_plane_restr0.007510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2968-2.36430.37841450.2969236086
2.3643-2.44060.28071170.22232697100
2.4406-2.52780.28051570.21022716100
2.5278-2.62890.27461650.22042728100
2.6289-2.74850.26941230.20972689100
2.7485-2.89330.30691520.20212736100
2.8933-3.07440.29711400.21672717100
3.0744-3.31150.23151420.20952707100
3.3115-3.64430.25621470.2012262397
3.6443-4.17040.24641420.1979271098
4.1704-5.24970.19481300.15352711100
5.2497-29.98640.21021550.19392674100
Refinement TLS params.Method: refined / Origin x: 36.9457 Å / Origin y: 1.1584 Å / Origin z: 54.2537 Å
111213212223313233
T0.056 Å20.0292 Å2-0.0009 Å2-0.0543 Å2-0.0026 Å2--0.0609 Å2
L0.0786 °2-0.0288 °2-0.0616 °2-0.0412 °2-0.0089 °2--0.3172 °2
S0.0205 Å °0.0002 Å °-0.031 Å °-0.0213 Å °-0.0142 Å °0.0229 Å °-0.0238 Å °0.0822 Å °0.031 Å °
Refinement TLS groupSelection details: all

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