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- PDB-8k7n: Structure of ferric-binding protein KfuA -

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Basic information

Entry
Database: PDB / ID: 8k7n
TitleStructure of ferric-binding protein KfuA
ComponentsFerric iron ABC transporter, iron-binding protein
KeywordsMETAL BINDING PROTEIN / Iron binding protein / ABC transporter
Function / homology
Function and homology information


iron ion transport / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Ferric binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature.
Similarity search - Domain/homology
: / Fe(3+)-binding periplasmic protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhao, Q. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
CitationJournal: To be published
Title: Structure of Klebsiella pneumoniae ferric-binding protein KfuA
Authors: Zhao, Q. / Bartlam, M.
History
DepositionJul 26, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric iron ABC transporter, iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6412
Polymers36,5851
Non-polymers561
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.275, 52.278, 56.392
Angle α, β, γ (deg.)90.000, 94.430, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ferric iron ABC transporter, iron-binding protein / Iron ABC transporter substrate-binding protein


Mass: 36585.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Klebsiella pneumoniae is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A288TNX3.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: fbpA, CWN47_21360, IAP99_17305, NCTC9178_03966 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A288TNX3
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium chloride, 25% w/v Polyethylene glycol 3,350 and 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→38.29 Å / Num. obs: 18079 / % possible obs: 96.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 22.78 Å2 / Rpim(I) all: 0.031 / Net I/σ(I): 20.6
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 882 / Rpim(I) all: 0.073

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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: 2→37.58 Å / SU ML: 0.1684 / Cross valid method: FREE R-VALUE / σ(F): 0.41 / Phase error: 19.3347
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1988 1805 10.02 %
Rwork0.1584 16214 -
obs0.1625 18019 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.59 Å2
Refinement stepCycle: LAST / Resolution: 2→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 1 284 2635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742402
X-RAY DIFFRACTIONf_angle_d0.86433259
X-RAY DIFFRACTIONf_chiral_restr0.0517360
X-RAY DIFFRACTIONf_plane_restr0.0047423
X-RAY DIFFRACTIONf_dihedral_angle_d14.256868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.22641330.16511185X-RAY DIFFRACTION92.49
2.05-2.120.22961400.16171236X-RAY DIFFRACTION97.59
2.12-2.180.23741460.16221249X-RAY DIFFRACTION96.41
2.18-2.260.21051350.15751267X-RAY DIFFRACTION96.82
2.26-2.350.2171480.161240X-RAY DIFFRACTION97.68
2.35-2.460.22461430.16521228X-RAY DIFFRACTION97.23
2.46-2.590.22811210.16971250X-RAY DIFFRACTION95.74
2.59-2.750.2151450.17471257X-RAY DIFFRACTION97.84
2.75-2.960.21591400.1781266X-RAY DIFFRACTION96.83
2.96-3.260.21991370.171212X-RAY DIFFRACTION95.2
3.26-3.730.18461370.14851292X-RAY DIFFRACTION98.48
3.73-4.70.15051400.13491262X-RAY DIFFRACTION96.16
4.7-37.580.17791400.15741270X-RAY DIFFRACTION95.08

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