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- PDB-5d1n: Crystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltran... -

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Basic information

Entry
Database: PDB / ID: 5d1n
TitleCrystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltransferase with its reaction by-product SAH from Catenulisporales acidiphilia
ComponentsUncharacterized protein
KeywordsTRANSFERASE / methyltransferase / ribosome / aminoglycoside resistance
Function / homologyVaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S-ADENOSYL-L-HOMOCYSTEINE / rRNA methyltransferase
Function and homology information
Biological speciesCatenulispora acidiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.713 Å
AuthorsWitek, M.A. / Conn, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI088025 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Functional dichotomy in the 16S rRNA (m1A1408) methyltransferase family and control of catalytic activity via a novel tryptophan mediated loop reorganization.
Authors: Witek, M.A. / Conn, G.L.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0112
Polymers28,6271
Non-polymers3841
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.739, 65.967, 82.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 28626.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catenulispora acidiphila (bacteria) / Strain: DSM 44928 / NRRL B-24433 / NBRC 102108 / JCM 14897 / Gene: Caci_9046 / Production host: Escherichia coli (E. coli) / References: UniProt: C7Q5P8
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.03 M BisTris, pH 5.5, 25.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 6715 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X1O

4x1o


Resolution: 2.713→41.436 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 634 10.06 %
Rwork0.2132 --
obs0.2202 6302 93.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.713→41.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 26 22 1709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021723
X-RAY DIFFRACTIONf_angle_d0.6632362
X-RAY DIFFRACTIONf_dihedral_angle_d11.284630
X-RAY DIFFRACTIONf_chiral_restr0.025285
X-RAY DIFFRACTIONf_plane_restr0.004300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7133-2.92280.38921140.275977X-RAY DIFFRACTION84
2.9228-3.21680.27371220.25151102X-RAY DIFFRACTION93
3.2168-3.6820.291270.20861154X-RAY DIFFRACTION97
3.682-4.6380.27211310.18951194X-RAY DIFFRACTION98
4.638-41.44080.25431400.20371241X-RAY DIFFRACTION97

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