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- PDB-6r4q: Crystal structure of the periplasmic nickel-binding protein NikA ... -

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Basic information

Entry
Database: PDB / ID: 6r4q
TitleCrystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl
ComponentsNickel-binding periplasmic protein
KeywordsMETAL BINDING PROTEIN / Artificial metalloenzyme / Ru-based oxidase / styrene oxidation
Function / homology
Function and homology information


nickel cation import across plasma membrane / metal cluster binding / 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
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: 1.9 Å
AuthorsCavazza, C. / Menage, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyCrystalball France
CitationJournal: To Be Published
Title: Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl
Authors: Cavazza, C. / Menage, S.
History
DepositionMar 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: 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)115,68436
Polymers112,7212
Non-polymers2,96234
Water13,295738
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,11221
Polymers56,3611
Non-polymers1,75120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-33 kcal/mol
Surface area20850 Å2
MethodPISA
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,57215
Polymers56,3611
Non-polymers1,21214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-18 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.629, 94.101, 124.418
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)
Strain: K12 / Gene: nikA, b3476, JW3441 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33590

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Non-polymers , 9 types, 772 molecules

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


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


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-RU / RUTHENIUM ION / Ruthenium


Mass: 101.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ru
#8: Chemical ChemComp-6RP / bis(pyrzol-1-yl)acetate scorpionate / BPZ


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


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M Na acetate pH 4.6 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979758 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979758 Å / Relative weight: 1
ReflectionResolution: 1.9→44.52 Å / Num. obs: 564360 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 16.06
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 11369

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZLQ

1zlq


Resolution: 1.9→44.52 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.208 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23191 4031 5 %RANDOM
Rwork0.17768 ---
obs0.18036 76571 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å2-0 Å2
2---0.84 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.9→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7864 0 186 738 8788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177596
X-RAY DIFFRACTIONr_angle_refined_deg1.561.6511283
X-RAY DIFFRACTIONr_angle_other_deg1.3291.5717685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05751017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04523.144423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.228151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5291543
X-RAY DIFFRACTIONr_chiral_restr0.0730.21081
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021664
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_it1.9152.3784018
X-RAY DIFFRACTIONr_mcbond_other1.8932.3714005
X-RAY DIFFRACTIONr_mcangle_it2.7683.5495014
X-RAY DIFFRACTIONr_mcangle_other2.7693.555013
X-RAY DIFFRACTIONr_scbond_it2.5992.6974280
X-RAY DIFFRACTIONr_scbond_other2.5992.6974281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9463.9176259
X-RAY DIFFRACTIONr_long_range_B_refined6.26729.2799602
X-RAY DIFFRACTIONr_long_range_B_other6.26729.2849603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 293 -
Rwork0.342 5563 -
obs--99.56 %

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