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- PDB-7og7: Crystal structure of the copper chaperone NosL from Shewanella de... -

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Basic information

Entry
Database: PDB / ID: 7og7
TitleCrystal structure of the copper chaperone NosL from Shewanella denitrificans
ComponentsNosL
KeywordsMETAL BINDING PROTEIN / copper chaperone
Function / homologyNitrous oxide reductase accessory protein NosL / NosL / ACETONITRILE / COPPER (I) ION / NosL
Function and homology information
Biological speciesShewanella denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsPrasser, B. / Schoener, L. / Zhang, L. / Einsle, O.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)310656 Germany
German Research Foundation (DFG)235777276 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: The Copper Chaperone NosL Forms a Heterometal Site for Cu Delivery to Nitrous Oxide Reductase.
Authors: Prasser, B. / Schoner, L. / Zhang, L. / Einsle, O.
History
DepositionMay 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NosL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6548
Polymers20,3201
Non-polymers3347
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-7 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.066, 179.066, 179.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-389-

HOH

21A-394-

HOH

31A-398-

HOH

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Components

#1: Protein NosL


Mass: 20320.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013) (bacteria)
Strain: OS217 / ATCC BAA-1090 / DSM 15013 / Gene: Sden_2215 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q12M31
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES buffer at pH 7.5 and 1.4 M trisodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.28096 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28096 Å / Relative weight: 1
ReflectionResolution: 1.85→44.77 Å / Num. obs: 21586 / % possible obs: 100 % / Redundancy: 76.6 % / CC1/2: 1 / Net I/σ(I): 35.3
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 1322 / CC1/2: 0.431

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→44.767 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 1947 4.91 %
Rwork0.1941 37670 -
obs0.1954 21586 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.79 Å2 / Biso mean: 35.9209 Å2 / Biso min: 20.35 Å2
Refinement stepCycle: final / Resolution: 1.85→44.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 32 102 1197
Biso mean--54.46 41.64 -
Num. residues----134
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8501-1.89630.29531300.32612662
1.8963-1.94760.32531750.29312699
1.9476-2.00490.27591530.27742654
2.0049-2.06960.26911350.25022701
2.0696-2.14360.26061340.22392705
2.1436-2.22940.22841180.20812691
2.2294-2.33090.24061280.19922696
2.3309-2.45380.19851310.19412692
2.4538-2.60750.27971270.19182689
2.6075-2.80880.21561430.20252713
2.8088-3.09140.20761610.21132666
3.0914-3.53860.23351480.1922690
3.5386-4.45760.16241250.14882697
4.4576-44.760.21231390.17252715

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