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- PDB-9t0x: Crystal structure of H416C NikA mutant from Escherichia coli cova... -

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Basic information

Entry
Database: PDB / ID: 9t0x
TitleCrystal structure of H416C NikA mutant from Escherichia coli covalently bound to a modified Mn(salen) complex
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
1-methylpyrrolidine-2,5-dione / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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)112,8784
Polymers112,6512
Non-polymers2262
Water5,783321
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4392
Polymers56,3261
Non-polymers1131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4392
Polymers56,3261
Non-polymers1131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.799, 93.229, 123.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nickel-binding periplasmic protein


Mass: 56325.730 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-LCY / 1-methylpyrrolidine-2,5-dione


Mass: 113.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.77 %
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: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.81→46.66 Å / Num. obs: 85875 / % possible obs: 95.2 % / Redundancy: 2.74 % / CC1/2: 0.99 / Net I/σ(I): 10.37
Reflection shellResolution: 1.81→1.92 Å / Mean I/σ(I) obs: 0.39 / Num. unique obs: 23198 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→46.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.99 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27613 1082 1.3 %RANDOM
Rwork0.21707 ---
obs0.21781 84800 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.137 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å2-0 Å20 Å2
2---2.6 Å2-0 Å2
3---1.51 Å2
Refinement stepCycle: 1 / Resolution: 1.81→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7916 0 0 321 8237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128314
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167924
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.82211327
X-RAY DIFFRACTIONr_angle_other_deg0.5561.75818311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.096550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89101427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.21263
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029688
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021868
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3434.6153982
X-RAY DIFFRACTIONr_mcbond_other4.3424.6153982
X-RAY DIFFRACTIONr_mcangle_it5.5388.2744974
X-RAY DIFFRACTIONr_mcangle_other5.5388.2754975
X-RAY DIFFRACTIONr_scbond_it4.7254.9644332
X-RAY DIFFRACTIONr_scbond_other4.7254.9654333
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5718.9626354
X-RAY DIFFRACTIONr_long_range_B_refined8.62447.089500
X-RAY DIFFRACTIONr_long_range_B_other8.62547.099477
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.856 Å
RfactorNum. reflection% reflection
Rfree0.423 69 -
Rwork0.47 5417 -
obs--82.45 %

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