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- PDB-5on9: Crystal structure of NikA in complex with reduced Fe-L1 (N-(2-hyd... -

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Basic information

Entry
Database: PDB / ID: 5on9
TitleCrystal structure of NikA in complex with reduced 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 transmembrane transporter activity / peptide transport / 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 transmembrane transporter activity / peptide transport / 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-9YH / ACETATE ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / 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 3, 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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Aug 19, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)115,19823
Polymers112,7212
Non-polymers2,47721
Water19,4741081
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,72513
Polymers56,3611
Non-polymers1,36512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,47310
Polymers56,3611
Non-polymers1,1129
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.900, 94.100, 124.700
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 , 7 types, 1102 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-9YH / 2-[2-[2-hydroxy-2-oxoethyl-[(3-methoxy-2-oxidanyl-phenyl)methyl]amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid


Mass: 448.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N2O6S
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1081 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM sodium acetate pH 4.6 1.7 ammonium sulfate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979763 Å / Relative weight: 1
ReflectionResolution: 1.7→47.05 Å / Num. obs: 112782 / % possible obs: 100 % / Redundancy: 7.36 % / Net I/σ(I): 20.69

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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→44.021 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.96
RfactorNum. reflection% reflection
Rfree0.2107 5638 5 %
Rwork0.1767 --
obs0.1784 112763 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→44.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7828 0 151 1081 9060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058359
X-RAY DIFFRACTIONf_angle_d0.95711417
X-RAY DIFFRACTIONf_dihedral_angle_d13.3653146
X-RAY DIFFRACTIONf_chiral_restr0.0371249
X-RAY DIFFRACTIONf_plane_restr0.0051496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.31711870.28023539X-RAY DIFFRACTION100
1.7193-1.73950.31831860.27113543X-RAY DIFFRACTION100
1.7395-1.76080.28481830.26533483X-RAY DIFFRACTION100
1.7608-1.78310.28061870.25753559X-RAY DIFFRACTION100
1.7831-1.80650.31021870.24883557X-RAY DIFFRACTION100
1.8065-1.83130.28931850.24283511X-RAY DIFFRACTION100
1.8313-1.85740.29381860.23283531X-RAY DIFFRACTION100
1.8574-1.88520.26731870.22063555X-RAY DIFFRACTION100
1.8852-1.91460.26881860.22083529X-RAY DIFFRACTION100
1.9146-1.9460.24551860.2053537X-RAY DIFFRACTION100
1.946-1.97960.26991870.2043548X-RAY DIFFRACTION100
1.9796-2.01560.23771870.20083549X-RAY DIFFRACTION100
2.0156-2.05430.24021870.18943554X-RAY DIFFRACTION100
2.0543-2.09620.22651850.18873524X-RAY DIFFRACTION100
2.0962-2.14180.23161870.1743561X-RAY DIFFRACTION100
2.1418-2.19160.21631870.17323541X-RAY DIFFRACTION100
2.1916-2.24650.21421870.17653548X-RAY DIFFRACTION100
2.2465-2.30720.20471870.17453551X-RAY DIFFRACTION100
2.3072-2.37510.22941880.17993583X-RAY DIFFRACTION100
2.3751-2.45170.20731870.17953559X-RAY DIFFRACTION100
2.4517-2.53940.21661880.17963564X-RAY DIFFRACTION100
2.5394-2.6410.23561890.17823584X-RAY DIFFRACTION100
2.641-2.76120.21881880.18423573X-RAY DIFFRACTION100
2.7612-2.90670.24211890.17873589X-RAY DIFFRACTION100
2.9067-3.08880.22011880.17663589X-RAY DIFFRACTION100
3.0888-3.32720.17931900.16363600X-RAY DIFFRACTION100
3.3272-3.66190.1771910.15393638X-RAY DIFFRACTION100
3.6619-4.19140.16181910.13413630X-RAY DIFFRACTION100
4.1914-5.27940.15811940.13913684X-RAY DIFFRACTION100
5.2794-44.03560.19172010.1783812X-RAY DIFFRACTION99

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