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- PDB-5l8d: X-ray structure of NikA from Escherichia coli in complex with Ru(... -

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Basic information

Entry
Database: PDB / ID: 5l8d
TitleX-ray structure of NikA from Escherichia coli in complex with Ru(bis(pyrzol-1-yl)acetate scorpionate)(CO)2Cl
ComponentsNickel-binding periplasmic protein
KeywordsMETAL BINDING PROTEIN / Nickel-binding protein / artificial enzymes / bio-inspired chemistry
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
bis(pyrzol-1-yl)acetate scorpionate / ACETATE ION / CARBON MONOXIDE / Chem-EDT / : / RUTHENIUM ION / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMenage, S. / Cavazza, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency14-CE06-0005-01 France
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: Efficient conversion of alkenes to chlorohydrins by a Ru-based artificial enzyme.
Authors: Lopez, S. / Rondot, L. / Cavazza, C. / Iannello, M. / Boeri-Erba, E. / Burzlaff, N. / Strinitz, F. / Jorge-Robin, A. / Marchi-Delapierre, C. / Menage, S.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Atomic model / Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5Jan 10, 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

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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)115,28133
Polymers112,7212
Non-polymers2,56031
Water11,998666
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,86318
Polymers56,3611
Non-polymers1,50217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,41915
Polymers56,3611
Non-polymers1,05814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.303, 93.606, 124.211
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 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33590

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Non-polymers , 10 types, 697 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#7: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ru
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-6RP / bis(pyrzol-1-yl)acetate scorpionate / BPZ


Mass: 192.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N4O2
#10: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.24 Å3/Da / Density % sol: 45.13 % / Description: Plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1.8 M ammonium sulfate, 100 mM sodium acetate pH 4.7

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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: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979763 Å / Relative weight: 1
ReflectionResolution: 1.8→46.8 Å / Num. obs: 92563 / % possible obs: 98.8 % / Redundancy: 4.98 % / Net I/σ(I): 21.24

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVW

3mvw


Resolution: 1.8→46.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.145 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.121
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 4629 5 %RANDOM
Rwork0.1677 ---
obs0.1697 87934 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.96 Å2 / Biso mean: 27.073 Å2 / Biso min: 14.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2---1.05 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.8→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7847 0 159 666 8672
Biso mean--44.17 34.62 -
Num. residues----996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198369
X-RAY DIFFRACTIONr_bond_other_d0.0010.027874
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.97211417
X-RAY DIFFRACTIONr_angle_other_deg2.347318166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60851052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32824.545385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.213151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4721545
X-RAY DIFFRACTIONr_chiral_restr0.1190.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0219533
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021896
X-RAY DIFFRACTIONr_mcbond_it2.4342.4854059
X-RAY DIFFRACTIONr_mcbond_other2.4122.4814050
X-RAY DIFFRACTIONr_mcangle_it3.2243.7045069
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 340 -
Rwork0.274 6457 -
all-6797 -
obs--99.68 %

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