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- PDB-6bri: RHCC with unreduced and reduced Mercury complexes -

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Basic information

Entry
Database: PDB / ID: 6bri
TitleRHCC with unreduced and reduced Mercury complexes
ComponentsRight Handed Coiled Coil
KeywordsMETAL BINDING PROTEIN / Archaea / Coiled-Coil / Nanotube / Nanoparticle / Mercury
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Tetrabrachion / Tetrabrachion / Tetrabrachion, parallel right-handed coiled coil domain / Tetrabrachion / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / MERCURY (II) IODIDE / mercuriomercury / IODIDE ION / : / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylothermus marinus F1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.266 Å
AuthorsMcDougall, M. / Trieu, B. / Stetefeld, J.
Funding support Canada, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-342077-2012 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-004954-2017 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)STGP 479210-2015 Canada
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Reductive power of the archaea right-handed coiled coil nanotube (RHCC-NT) and incorporation of mercury clusters inside protein cages.
Authors: McDougall, M. / McEleney, K. / Francisco, O. / Trieu, B. / Ogbomo, E.K. / Tomy, G. / Stetefeld, J.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Right Handed Coiled Coil
B: Right Handed Coiled Coil
C: Right Handed Coiled Coil
D: Right Handed Coiled Coil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,66434
Polymers23,5954
Non-polymers4,06930
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-129 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.823, 108.823, 70.388
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Right Handed Coiled Coil


Mass: 5898.720 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylothermus marinus F1 (archaea) / Strain: ATCC 43588 / DSM 3639 / JCM 9404 / F1 / Gene: Smar_1008 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DN96

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Non-polymers , 8 types, 30 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-HGN / mercuriomercury


Mass: 401.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-HGI / MERCURY (II) IODIDE / MERCURY DIIODIDE / Mercury(II) iodide


Mass: 454.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HgI2

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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: 5.24 Å3/Da / Density % sol: 76.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 2M Ammonium Sulfate 200 mM Tris pH 7.9 0.7mM K2HgI4 soaked in 4 days prior to collection

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8472 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8472 Å / Relative weight: 1
ReflectionResolution: 3.266→28.69 Å / Num. obs: 7550 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 3.8
Reflection shellResolution: 3.266→3.35 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.8 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YBK

1ybk


Resolution: 3.266→28.687 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2998 785 10.48 %
Rwork0.2817 --
obs0.2836 7494 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.266→28.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 48 0 1580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021558
X-RAY DIFFRACTIONf_angle_d0.5052108
X-RAY DIFFRACTIONf_dihedral_angle_d26.651565
X-RAY DIFFRACTIONf_chiral_restr0.035276
X-RAY DIFFRACTIONf_plane_restr0.002266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2657-3.470.38651200.34821019X-RAY DIFFRACTION90
3.47-3.73740.37151240.32671119X-RAY DIFFRACTION99
3.7374-4.11260.31971540.31631109X-RAY DIFFRACTION99
4.1126-4.70540.351260.27861154X-RAY DIFFRACTION100
4.7054-5.91970.25031320.26411163X-RAY DIFFRACTION100
5.9197-28.68820.21231290.22131145X-RAY DIFFRACTION95

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