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- PDB-9t0v: Crystal structure of H416C NikA mutant from Escherichia coli in c... -

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Basic information

Entry
Database: PDB / ID: 9t0v
TitleCrystal structure of H416C NikA mutant from Escherichia coli in complex with Fe(III)-EDTA
ComponentsNickel-binding periplasmic protein
KeywordsMETAL BINDING PROTEIN / Nickel importer Fe(III)-EDTA binding His416Cys mutation
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-EDT / : / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.542 Å
AuthorsCavazza, C. / Menage, S.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)INCA France
CitationJournal: Chemistry / Year: 2026
Title: Covalent Insertion of a Mn(Salen) Type Complex in Cross-Linked Protein Crystals: Design of an Enantioselective Artificial Epoxidase.
Authors: Boukhallat, M. / Benhamed, I. / Arnone, J. / Van Baaren, S. / Rinaldi, C. / Catty, P. / Marchi-Delapierre, C. / Cavazza, C. / Menage, S.
History
DepositionOct 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)113,87413
Polymers112,6512
Non-polymers1,22211
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.688, 94.924, 124.183
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: 56325.730 Da / Num. of mol.: 2 / Mutation: H416C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: nikA, b3476, JW3441 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33590

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Non-polymers , 7 types, 189 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.9 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: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.54→47.46 Å / Num. obs: 34187 / % possible obs: 99.21 % / Redundancy: 6.62 % / CC1/2: 0.97 / Net I/σ(I): 4.9
Reflection shellResolution: 2.54→2.7 Å / Num. unique obs: 5256 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.542→44.569 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1651 4.83 %RANDOM
Rwork0.2037 ---
obs0.2064 34159 99.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.542→44.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7877 0 74 178 8129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038211
X-RAY DIFFRACTIONf_angle_d0.71811178
X-RAY DIFFRACTIONf_dihedral_angle_d5.3386878
X-RAY DIFFRACTIONf_chiral_restr0.0511231
X-RAY DIFFRACTIONf_plane_restr0.0051457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.542-2.61650.41061230.33922480X-RAY DIFFRACTION92
2.6165-2.70090.33141290.27562690X-RAY DIFFRACTION100
2.7009-2.79740.29591300.27462703X-RAY DIFFRACTION100
2.7974-2.90940.35921240.26642666X-RAY DIFFRACTION100
2.9094-3.04180.31251470.25582694X-RAY DIFFRACTION100
3.0418-3.20210.34851410.23352714X-RAY DIFFRACTION100
3.2021-3.40270.30291470.21472679X-RAY DIFFRACTION100
3.4027-3.66530.26311460.20012732X-RAY DIFFRACTION100
3.6653-4.03390.23871370.1812715X-RAY DIFFRACTION100
4.0339-4.61710.18871340.15212751X-RAY DIFFRACTION100
4.6171-5.81510.2121480.16612782X-RAY DIFFRACTION100
5.8151-44.5690.19381450.18272902X-RAY DIFFRACTION100

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