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- PDB-5d1h: Crystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltran... -

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Basic information

Entry
Database: PDB / ID: 5d1h
TitleCrystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltransferase W203A mutant 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 / rRNA methyltransferase
Function and homology information
Biological speciesCatenulispora acidiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 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 27, 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
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)57,0232
Polymers57,0232
Non-polymers00
Water18010
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,5111
Polymers28,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,5111
Polymers28,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.007, 84.112, 94.368
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: 28511.477 Da / Num. of mol.: 2 / Mutation: W203A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium Acetate, 0.1 M Sodium Acetate Trihydrate, 30% PEG

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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: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13446 / % possible obs: 92.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.6
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / % possible all: 92.4

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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: 2.803→42.056 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 1220 9.99 %
Rwork0.1829 --
obs0.188 12210 91.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.803→42.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 0 10 3085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033134
X-RAY DIFFRACTIONf_angle_d0.7544290
X-RAY DIFFRACTIONf_dihedral_angle_d12.3541144
X-RAY DIFFRACTIONf_chiral_restr0.029524
X-RAY DIFFRACTIONf_plane_restr0.005547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8034-2.91560.34551220.25281136X-RAY DIFFRACTION87
2.9156-3.04830.28211320.2491186X-RAY DIFFRACTION90
3.0483-3.20890.30511310.22871182X-RAY DIFFRACTION91
3.2089-3.40990.26581370.19721223X-RAY DIFFRACTION92
3.4099-3.6730.25031370.18681232X-RAY DIFFRACTION92
3.673-4.04240.20981390.16261240X-RAY DIFFRACTION94
4.0424-4.62670.19041380.14611253X-RAY DIFFRACTION93
4.6267-5.82670.22161400.16091254X-RAY DIFFRACTION92
5.8267-42.06070.19871440.18231284X-RAY DIFFRACTION89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8066-0.9974-0.47773.84911.31121.9240.0090.42120.3162-0.8944-0.00820.1946-0.45310.3111-0.04990.42940.0241-0.05350.50910.12780.2963-9.5563-10.3089-11.0624
23.13710.11930.23632.6535-0.49313.1025-0.29570.3152-0.2397-0.18360.1889-0.07140.63580.33250.01860.3249-0.00920.01860.41870.01470.2616-9.3256-21.0403-7.0605
33.1434-0.64950.60860.58840.37863.2937-0.2526-0.09870.00330.08660.15650.01330.03620.16210.0020.28080.0120.04090.19580.04510.2523-1.9428-19.189112.3568
43.1-1.50880.04582.5422-0.13794.149-0.4861-0.1975-0.3297-0.03320.14570.3664-0.1594-0.0319-0.0560.17110.03910.05270.19380.14390.4363-8.0866-17.476715.7549
52.7215-0.4002-0.89540.9332-0.43551.6715-0.0472-0.5794-0.29180.1111-0.0631-0.00720.11130.06740.0230.40320.02410.06080.53030.20380.3718-16.6145-28.553850.8413
62.60270.1987-0.011.7284-0.26592.5965-0.1006-0.13330.1947-0.015-0.10740.0104-0.29150.08250.16370.2630.0580.00310.20780.03170.2582-9.1902-14.063536.5692
75.2941-1.9467-0.76724.8291.04391.2901-0.2178-0.62760.35990.87670.230.4322-0.2179-0.41060.19650.93460.48420.07190.5397-0.07470.4636-17.2552-2.599743.7733
86.11886.5590.64739.23080.02641.6851-0.14650.3566-0.6937-1.38190.3652-0.20830.458-0.4166-0.2520.36540.0191-0.08920.3721-0.01730.2698-18.714-21.063227.7019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:32)
2X-RAY DIFFRACTION2(chain A and resid 33:94)
3X-RAY DIFFRACTION3(chain A and resid 95:192)
4X-RAY DIFFRACTION4(chain A and resid 212:227)
5X-RAY DIFFRACTION5(chain B and resid 8:97)
6X-RAY DIFFRACTION6(chain B and resid 98:188)
7X-RAY DIFFRACTION7(chain B and resid 189:217)
8X-RAY DIFFRACTION8(chain B and resid 218:226)

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