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- PDB-7a0c: X-ray structure of NikA from Escherichia coli in complex with Fe-... -

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Basic information

Entry
Database: PDB / ID: 7a0c
TitleX-ray structure of NikA from Escherichia coli in complex with Fe-6-Me2-BPMCN
ComponentsNickel-binding periplasmic protein
KeywordsMETAL BINDING PROTEIN / Artificial metalloenzyme / cross-linked enzyme crystal / sulfoxidation
Function / homology
Function and homology information


nickel cation import across plasma membrane / metal cluster binding / nickel cation transport / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space ...nickel cation import across plasma membrane / metal cluster binding / nickel cation transport / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / periplasmic space / heme binding / membrane
Similarity search - Function
Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle
Similarity search - Domain/homology
ACETATE ION / : / Chem-QTT / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCavazza, C. / Menage, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE07-0034-02 France
CitationJournal: Chemistry / Year: 2020
Title: A Selective Sulfide Oxidation Catalyzed by Heterogeneous Artificial Metalloenzymes Iron@NikA.
Authors: Lopez, S. / Marchi-Delapierre, C. / Cavazza, C. / Menage, S.
History
DepositionAug 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: 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: Nickel-binding periplasmic protein
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,14330
Polymers112,7212
Non-polymers2,42228
Water14,322795
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,82918
Polymers56,3611
Non-polymers1,46917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,31412
Polymers56,3611
Non-polymers95311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.809, 93.796, 124.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nickel-binding periplasmic protein


Mass: 56360.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: nikA, b3476, JW3441 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33590

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Non-polymers , 7 types, 823 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-QTT / 2-[[(1~{S},2~{S})-2-[methyl-[(6-methylpyridin-2-yl)methyl]amino]cyclohexyl]-[(6-methylpyridin-2-yl)methyl]amino]ethanoic acid


Mass: 396.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H32N4O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.7 M Ammonium sulfate, 100 mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.9→43.875 Å / Num. obs: 80337 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rsym value: 9.6 / Net I/σ(I): 13.06
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 11314 / CC1/2: 0.655 / Rsym value: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZLQ

1zlq


Resolution: 1.9→43.875 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 4017 5 %
Rwork0.1815 76320 -
obs0.1835 80337 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.17 Å2 / Biso mean: 30.3509 Å2 / Biso min: 12.81 Å2
Refinement stepCycle: final / Resolution: 1.9→43.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7904 0 156 795 8855
Biso mean--42.19 37.13 -
Num. residues----996
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92240.37111370.2952604100
1.9224-1.94580.33671360.27832589100
1.9458-1.97040.3051380.26782622100
1.9704-1.99640.32871370.26812609100
1.9964-2.02370.29561360.25122583100
2.0237-2.05260.34861360.242570100
2.0526-2.08330.23931370.22812613100
2.0833-2.11580.29731380.22352617100
2.1158-2.15050.27231370.20872609100
2.1505-2.18760.27641380.21312610100
2.1876-2.22740.26471380.20512631100
2.2274-2.27020.23581360.20492588100
2.2702-2.31650.251380.20282613100
2.3165-2.36690.26611390.18892635100
2.3669-2.42190.27341360.19722599100
2.4219-2.48250.22591390.1872636100
2.4825-2.54960.23911380.18732620100
2.5496-2.62460.22381370.18242610100
2.6246-2.70930.21571400.18892654100
2.7093-2.80620.24681370.19142605100
2.8062-2.91850.24451400.18612657100
2.9185-3.05130.21491380.1792619100
3.0513-3.21210.22181390.17122646100
3.2121-3.41330.20421390.15932636100
3.4133-3.67670.18161400.15142667100
3.6767-4.04650.16121410.13762673100
4.0465-4.63150.14341410.13832675100
4.6315-5.8330.18871430.16362726100
5.833-100.2331480.1868280498

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