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- PDB-5fh9: Crystal structure of NFeoB from Escherichia coli BL21 in the apo ... -

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Basic information

Entry
Database: PDB / ID: 5fh9
TitleCrystal structure of NFeoB from Escherichia coli BL21 in the apo state.
ComponentsFerrous iron transport protein B
KeywordsMETAL TRANSPORT / GTPase
Function / homology
Function and homology information


: / ferrous iron transmembrane transporter activity / membrane => GO:0016020 / GTP binding / plasma membrane
Similarity search - Function
Helix Hairpins - #1770 / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain ...Helix Hairpins - #1770 / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ferrous iron transport protein B
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.159 Å
AuthorsHagelueken, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB813 C8 Germany
CitationJournal: Biophys.J. / Year: 2016
Title: Studies on the X-Ray and Solution Structure of FeoB from Escherichia coli BL21.
Authors: Hagelueken, G. / Hoffmann, J. / Schubert, E. / Duthie, F.G. / Florin, N. / Konrad, L. / Imhof, D. / Behrmann, E. / Morgner, N. / Schiemann, O.
History
DepositionDec 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrous iron transport protein B
B: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)60,1412
Polymers60,1412
Non-polymers00
Water0
1
A: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)30,0701
Polymers30,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferrous iron transport protein B


Theoretical massNumber of molelcules
Total (without water)30,0701
Polymers30,0701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.675, 166.675, 65.581
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Ferrous iron transport protein B


Mass: 30070.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21 (bacteria) / Gene: feoB / Production host: Escherichia coli (E. coli) / References: UniProt: J7QA66

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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: 4.37 Å3/Da / Density % sol: 71.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 26.9 % PEG 8000, 0.39 M MgCl2, 0.1 M Tris-HCl pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9085 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9085 Å / Relative weight: 1
ReflectionResolution: 3.159→48.12 Å / Num. obs: 18052 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.2328 / Net I/σ(I): 9.11
Reflection shellResolution: 3.159→3.272 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.384 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 3.159→48.115 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 903 5 %
Rwork0.2078 --
obs0.2088 18049 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.159→48.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 0 0 4011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044064
X-RAY DIFFRACTIONf_angle_d0.7525518
X-RAY DIFFRACTIONf_dihedral_angle_d12.5032496
X-RAY DIFFRACTIONf_chiral_restr0.043663
X-RAY DIFFRACTIONf_plane_restr0.004714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.159-3.35690.36421470.32322792X-RAY DIFFRACTION98
3.3569-3.6160.28351500.25332842X-RAY DIFFRACTION100
3.616-3.97970.22841490.22592845X-RAY DIFFRACTION100
3.9797-4.55520.19561500.18362850X-RAY DIFFRACTION100
4.5552-5.73760.21891520.18622877X-RAY DIFFRACTION100
5.7376-48.12050.21550.17792940X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.2261 Å / Origin y: 124.0805 Å / Origin z: -68.1904 Å
111213212223313233
T0.7044 Å2-0.0262 Å2-0.0738 Å2-0.316 Å2-0.0383 Å2--0.5016 Å2
L0.0693 °2-0.1717 °2-0.0997 °2-1.4461 °2-0.9314 °2--1.8372 °2
S-0.0049 Å °0.0767 Å °0.0218 Å °-0.2032 Å °0.0648 Å °-0.0535 Å °-0.1718 Å °-0.0136 Å °-0.0429 Å °
Refinement TLS groupSelection details: ALL

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