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- PDB-4fak: Crystal Structure of OrfX in Complex with S-Adenosylmethionine -

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Basic information

Entry
Database: PDB / ID: 4fak
TitleCrystal Structure of OrfX in Complex with S-Adenosylmethionine
ComponentsRibosomal RNA large subunit methyltransferase H
KeywordsTRANSFERASE / RIBOSOMAL PROTEIN / alpha/beta methyltransferase Rossmann fold / rRNA methylation / AdoMet / rRNA
Function / homology
Function and homology information


23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / cytoplasm
Similarity search - Function
RNA methyltransferase RlmH / Predicted SPOUT methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYLMETHIONINE / Ribosomal RNA large subunit methyltransferase H
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSafo, M.K. / Musayev, F.N. / Boundy, S. / Archer, G.L. / Rife, J.P. / O'Farrell, H.C.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Characterization of the Staphylococcus aureus rRNA Methyltransferase Encoded by orfX, the Gene Containing the Staphylococcal Chromosome Cassette mec (SCCmec) Insertion Site.
Authors: Boundy, S. / Safo, M.K. / Wang, L. / Musayev, F.N. / O'Farrell, H.C. / Rife, J.P. / Archer, G.L.
History
DepositionMay 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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 H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4404
Polymers18,7531
Non-polymers6883
Water3,189177
1
A: Ribosomal RNA large subunit methyltransferase H
hetero molecules

A: Ribosomal RNA large subunit methyltransferase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8818
Polymers37,5062
Non-polymers1,3756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2990 Å2
ΔGint-23 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.800, 84.290, 55.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-302-

HOH

31A-426-

HOH

41A-446-

HOH

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Components

#1: Protein 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: 18752.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: RN450M / Gene: orfx, rlmH / Plasmid: pET30a / Production host: Escherichia coli (E. coli)
References: UniProt: P0C1V0, 23S rRNA (pseudouridine1915-N3)-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 550 MME, 5 mM ZnSO4, 0.1M Na 2-(N-morpholino) ethanesulfonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 1, 2010 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→28.6 Å / Num. all: 19664 / Num. obs: 20528 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.5
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1862 / % possible all: 93.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VH0

1vh0


Resolution: 1.7→26.43 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1372577.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1008 5.1 %RANDOM
Rwork0.207 ---
all0.214 19664 --
obs0.207 19662 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.9051 Å2 / ksol: 0.355692 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20 Å2
2--5.35 Å20 Å2
3----3.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 1.7→26.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 45 177 1536
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.181.5
X-RAY DIFFRACTIONc_mcangle_it3.872
X-RAY DIFFRACTIONc_scbond_it5.162
X-RAY DIFFRACTIONc_scangle_it6.932.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.376 97 5.2 %
Rwork0.366 1761 -
obs--93.7 %

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