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- PDB-6n0s: N-terminal domain of Staphylothermus marinus McrB -

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Basic information

Entry
Database: PDB / ID: 6n0s
TitleN-terminal domain of Staphylothermus marinus McrB
ComponentsATPase associated with various cellular activities, AAA_5
KeywordsDNA BINDING PROTEIN / EVE domain / restriction endonuclease
Function / homologyATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / ATP hydrolysis activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ATPase associated with various cellular activities, AAA_5
Function and homology information
Biological speciesStaphylothermus marinus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsHosford, C.J. / Niu, Y. / Chappie, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120242 United States
CitationJournal: J.Struct.Biol. / Year: 2020
Title: The N-terminal domain of Staphylothermus marinus McrB shares structural homology with PUA-like RNA binding proteins.
Authors: Hosford, C.J. / Adams, M.C. / Niu, Y. / Chappie, J.S.
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase associated with various cellular activities, AAA_5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7743
Polymers21,5821
Non-polymers1922
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-28 kcal/mol
Surface area9860 Å2
Unit cell
Length a, b, c (Å)62.406, 62.406, 118.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-382-

HOH

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Components

#1: Protein ATPase associated with various cellular activities, AAA_5 / McrB


Mass: 21581.625 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 3-180)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1) (archaea)
Strain: ATCC 43588 / DSM 3639 / JCM 9404 / F1 / Gene: Smar_0573 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3DM20
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-Tris propane, pH 7.5, 0.2 M sodium sulfate, 23% PEG3350
PH range: 7.3 - 7.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 19, 2017
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.92→55.26 Å / Num. obs: 29031 / % possible obs: 99.9 % / Redundancy: 42.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 19.9
Reflection shellResolution: 1.92→2.09 Å / Redundancy: 24.2 % / Rmerge(I) obs: 1.068 / Mean I/σ(I) obs: 3.63 / Num. unique obs: 8197 / CC1/2: 0.964 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.92→55.26 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2356 --
Rwork0.1964 --
obs-29031 99.9 %
Refinement stepCycle: LAST / Resolution: 2.1→55.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 10 94 1626
LS refinement shellHighest resolution: 1.92 Å

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