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- PDB-9d8b: High-resolution crystal structure of Vibrio cholerae NFeoB in the... -

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Basic information

Entry
Database: PDB / ID: 9d8b
TitleHigh-resolution crystal structure of Vibrio cholerae NFeoB in the GDP-bound form
ComponentsFerrous iron transport protein B
KeywordsTRANSPORT PROTEIN / Feo / iron / transport
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
FeoB, cytosolic helical domain / FeoB cytosolic helical domain / 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 / GTP binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ferrous iron transport protein B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLee, M. / Magante, K.D. / Smith, A.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133497 United States
National Science Foundation (NSF, United States)CHE1844624 United States
CitationJournal: To Be Published
Title: High-resolution crystal structure of Vibrio cholerae NFeoB in the GDP-bound form
Authors: Lee, M. / Magante, K.D. / Smith, A.T.
History
DepositionAug 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferrous iron transport protein B
B: Ferrous iron transport protein B
C: Ferrous iron transport protein B
D: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,81615
Polymers117,3984
Non-polymers2,41711
Water4,107228
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9774
Polymers29,3501
Non-polymers6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8853
Polymers29,3501
Non-polymers5352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0695
Polymers29,3501
Non-polymers7194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8853
Polymers29,3501
Non-polymers5352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.046, 59.024, 89.481
Angle α, β, γ (deg.)94.390, 92.980, 113.210
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Ferrous iron transport protein B


Mass: 29349.588 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: feoB_1, ERS013165_00117 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A655NVH2
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 28 % (w/v) PEG 4000, 0.1 M bicine (pH 8.4), 0.2 M ammonium acetate, 0.003 M GDP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979361 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979361 Å / Relative weight: 1
ReflectionResolution: 1.818→32.645 Å / Num. obs: 85262 / % possible obs: 93.9 % / Redundancy: 1.8 % / Biso Wilson estimate: 37.09 Å2 / CC1/2: 0.997 / Net I/σ(I): 4.2
Reflection shellResolution: 1.818→1.849 Å / Num. unique obs: 4302 / CC1/2: 0.452

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→30.83 Å / SU ML: 0.2844 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.5775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 4096 4.82 %
Rwork0.2029 80820 -
obs0.205 84916 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.99 Å2
Refinement stepCycle: LAST / Resolution: 1.82→30.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7817 0 154 228 8199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838086
X-RAY DIFFRACTIONf_angle_d1.122110932
X-RAY DIFFRACTIONf_chiral_restr0.06751279
X-RAY DIFFRACTIONf_plane_restr0.01621386
X-RAY DIFFRACTIONf_dihedral_angle_d12.15041132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.840.33141210.38872649X-RAY DIFFRACTION88.05
1.84-1.860.39061320.38252694X-RAY DIFFRACTION90.46
1.86-1.890.39641490.35332803X-RAY DIFFRACTION94.71
1.89-1.910.33481370.31872845X-RAY DIFFRACTION94.88
1.91-1.940.33411360.31212810X-RAY DIFFRACTION94.24
1.94-1.960.32211480.29262832X-RAY DIFFRACTION94.9
1.96-1.990.32831380.27952805X-RAY DIFFRACTION94.84
1.99-2.020.32461360.27212861X-RAY DIFFRACTION95.02
2.02-2.060.31421570.26652811X-RAY DIFFRACTION94.85
2.06-2.090.31161430.25742876X-RAY DIFFRACTION95.36
2.09-2.130.3171470.24562827X-RAY DIFFRACTION95.26
2.13-2.170.2741290.23982861X-RAY DIFFRACTION95.19
2.17-2.220.28321410.25142794X-RAY DIFFRACTION94.68
2.22-2.260.27591260.24212742X-RAY DIFFRACTION91.08
2.26-2.320.27521370.22322825X-RAY DIFFRACTION94.97
2.32-2.370.28611800.22792799X-RAY DIFFRACTION94.96
2.37-2.440.26051260.2242812X-RAY DIFFRACTION93.69
2.44-2.510.27361500.232781X-RAY DIFFRACTION94.34
2.51-2.590.24031290.22692849X-RAY DIFFRACTION94.15
2.59-2.680.28741340.22762818X-RAY DIFFRACTION93.74
2.68-2.790.26451430.22662790X-RAY DIFFRACTION93.68
2.79-2.920.25261630.21142742X-RAY DIFFRACTION93.56
2.92-3.070.26931630.20112735X-RAY DIFFRACTION92.85
3.07-3.260.24011490.20222761X-RAY DIFFRACTION92.41
3.26-3.520.20551230.19252726X-RAY DIFFRACTION91.31
3.52-3.870.22661540.17452712X-RAY DIFFRACTION91.1
3.87-4.430.19311300.15682724X-RAY DIFFRACTION91.07
4.43-5.570.21121470.16592752X-RAY DIFFRACTION92.83
5.57-30.830.24051280.17412784X-RAY DIFFRACTION92.86

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