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- PDB-8k8l: Structure of Klebsiella pneumonia ModA with molybdate -

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Basic information

Entry
Database: PDB / ID: 8k8l
TitleStructure of Klebsiella pneumonia ModA with molybdate
ComponentsMolybdate transporter periplasmic protein
KeywordsMETAL BINDING PROTEIN / Molybdate binding protein
Function / homologyMolybdate ABC transporter, substrate-binding protein / molybdate ion binding / : / Bacterial extracellular solute-binding protein / molybdate ion transport / outer membrane-bounded periplasmic space / metal ion binding / MOLYBDATE ION / Molybdate transporter periplasmic protein
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsZhao, Q. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural analysis of molybdate binding protein ModA from Klebsiella pneumoniae.
Authors: Zhao, Q. / Su, X. / Wang, Y. / Liu, R. / Bartlam, M.
History
DepositionJul 31, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdate transporter periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1692
Polymers27,0091
Non-polymers1601
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-2 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.102, 72.775, 125.234
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Molybdate transporter periplasmic protein


Mass: 27008.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) (bacteria)
Gene: KPHS_16010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GU89
#2: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3
Details: 0.1 M Citric acid, 25% w/v Polyethylene glycol 3,350, molybdate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 20631 / % possible obs: 98.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.64 Å2 / Rpim(I) all: 0.036 / Net I/σ(I): 16.7
Reflection shellResolution: 1.77→1.83 Å / Num. unique obs: 2045 / Rpim(I) all: 0.149

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→28.76 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 19.7607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2025 1926 9.34 %
Rwork0.1704 18699 -
obs0.1733 20625 79.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.77 Å2
Refinement stepCycle: LAST / Resolution: 1.77→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 5 275 2006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641764
X-RAY DIFFRACTIONf_angle_d0.86532397
X-RAY DIFFRACTIONf_chiral_restr0.059274
X-RAY DIFFRACTIONf_plane_restr0.0083309
X-RAY DIFFRACTIONf_dihedral_angle_d14.3084633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.28641340.22411279X-RAY DIFFRACTION78.72
1.81-1.860.2571560.211470X-RAY DIFFRACTION87.94
1.86-1.90.3186440.2502454X-RAY DIFFRACTION37.47
1.93-1.980.24171100.18571058X-RAY DIFFRACTION71.74
1.98-2.050.25141590.18471570X-RAY DIFFRACTION95.58
2.05-2.130.189980.1742918X-RAY DIFFRACTION55.1
2.13-2.230.20691640.16851611X-RAY DIFFRACTION97.47
2.23-2.350.22471160.17931138X-RAY DIFFRACTION67.27
2.35-2.490.21191670.17461614X-RAY DIFFRACTION97.8
2.49-2.650.21251410.18911363X-RAY DIFFRACTION98.11
2.7-2.960.24011620.18271585X-RAY DIFFRACTION98.59
2.96-3.380.20411740.17291695X-RAY DIFFRACTION99.05
3.38-4.260.15171150.14371132X-RAY DIFFRACTION65.6
4.26-28.760.16291860.14751812X-RAY DIFFRACTION98.09

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