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- PDB-5on1: Crystal structure of NikA in complex with hydroxylated Fe-L1 (N-(... -

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Basic information

Entry
Database: PDB / ID: 5on1
TitleCrystal structure of NikA in complex with hydroxylated Fe-L1 (N-(2-hydroxybenzyl)-N'-(2-thiomethylbenzyl)-N,N'-ethylenediamine diacetic acid)
ComponentsNickel-binding periplasmic protein
KeywordsMETAL BINDING PROTEIN / artificial oxygenase / CLEC / dioxygen activation / oxidation of carbon-carbon double bonds
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. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / 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 / Periplasmic binding protein-like II ...Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9YK / ACETATE ION / DITHIANE DIOL / : / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCavazza, C. / Menage, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE06-0005-01 France
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Cross-Linked Artificial Enzyme Crystals as Heterogeneous Catalysts for Oxidation Reactions.
Authors: Lopez, S. / Rondot, L. / Lepretre, C. / Marchi-Delapierre, C. / Menage, S. / Cavazza, C.
History
DepositionAug 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Aug 19, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.5Jan 17, 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)116,02037
Polymers112,7212
Non-polymers3,29935
Water15,295849
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,51926
Polymers56,3611
Non-polymers2,15825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,50211
Polymers56,3611
Non-polymers1,14110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.138, 94.896, 125.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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)
Gene: nikA, b3476, JW3441 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33590

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Non-polymers , 8 types, 884 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-9YK / 2-[2-[[2,3-bis(oxidanyl)phenyl]methyl-(2-hydroxy-2-oxoethyl)amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid


Mass: 434.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26N2O6S
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium acetate 100 mM, pH 4.6 Ammonium sulfate 1.7 M

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.7→44.83 Å / Num. obs: 114445 / % possible obs: 99.9 % / Redundancy: 6.52 % / Net I/σ(I): 28.28

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVW

3mvw


Resolution: 1.7→38.223 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.65
RfactorNum. reflection% reflection
Rfree0.2052 5722 5 %
Rwork0.1755 --
obs0.177 114439 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→38.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7838 0 200 849 8887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058368
X-RAY DIFFRACTIONf_angle_d0.94811410
X-RAY DIFFRACTIONf_dihedral_angle_d13.223131
X-RAY DIFFRACTIONf_chiral_restr0.0371239
X-RAY DIFFRACTIONf_plane_restr0.0051492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.3011880.2633564X-RAY DIFFRACTION100
1.7193-1.73960.28961900.25653612X-RAY DIFFRACTION100
1.7396-1.76080.26711880.24523563X-RAY DIFFRACTION100
1.7608-1.78310.31031880.23853585X-RAY DIFFRACTION100
1.7831-1.80650.25031900.23313595X-RAY DIFFRACTION100
1.8065-1.83130.26691870.2283571X-RAY DIFFRACTION100
1.8313-1.85740.31471900.23933601X-RAY DIFFRACTION100
1.8574-1.88520.2861890.23063591X-RAY DIFFRACTION100
1.8852-1.91460.27511890.21333591X-RAY DIFFRACTION100
1.9146-1.9460.25811900.20863607X-RAY DIFFRACTION100
1.946-1.97950.24151900.20513607X-RAY DIFFRACTION100
1.9795-2.01550.24721890.21093599X-RAY DIFFRACTION100
2.0155-2.05430.22731870.20153553X-RAY DIFFRACTION100
2.0543-2.09620.24641910.19513631X-RAY DIFFRACTION100
2.0962-2.14180.2241890.18423587X-RAY DIFFRACTION100
2.1418-2.19160.24251910.1883637X-RAY DIFFRACTION100
2.1916-2.24640.22351900.19843601X-RAY DIFFRACTION100
2.2464-2.30720.24331900.1923617X-RAY DIFFRACTION100
2.3072-2.3750.2231900.18943607X-RAY DIFFRACTION100
2.375-2.45170.20081900.1853609X-RAY DIFFRACTION100
2.4517-2.53930.21891910.19153617X-RAY DIFFRACTION100
2.5393-2.64090.21891910.18173646X-RAY DIFFRACTION100
2.6409-2.76110.23391910.18723629X-RAY DIFFRACTION100
2.7611-2.90660.20911920.18563636X-RAY DIFFRACTION100
2.9066-3.08870.20571920.17513644X-RAY DIFFRACTION100
3.0887-3.3270.20381920.16473652X-RAY DIFFRACTION100
3.327-3.66160.18531940.1553681X-RAY DIFFRACTION100
3.6616-4.19090.15081930.13743676X-RAY DIFFRACTION100
4.1909-5.27780.17021960.14093731X-RAY DIFFRACTION100
5.2778-38.23310.17112040.16963877X-RAY DIFFRACTION100

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