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- PDB-9psd: High-resolution crystal structure of Vibrio cholerae NFeoB bound ... -

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Basic information

Entry
Database: PDB / ID: 9psd
TitleHigh-resolution crystal structure of Vibrio cholerae NFeoB bound to GDP-AlF3
ComponentsFerrous iron transport protein B
KeywordsMETAL TRANSPORT / FEO / iron / membrane protein / transporter / GTPase / NTPase
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
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Ferrous iron transport protein B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMagante, K. / Lee, M. / Smith, A.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133497 United States
CitationJournal: J.Mol.Biol. / Year: 2026
Title: The Structure of the Full Catalytic Cycle of Vibrio cholerae NFeoB.
Authors: Magante, K. / Armstrong, C.M. / Lee, M. / Smith, A.T.
History
DepositionJul 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: 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)119,58014
Polymers117,3984
Non-polymers2,18210
Water11,133618
1
A: 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
2
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9935
Polymers29,3501
Non-polymers6444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9094
Polymers29,3501
Non-polymers5603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7932
Polymers29,3501
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.238, 59.077, 89.634
Angle α, β, γ (deg.)94.439, 92.373, 113.535
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 628 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25 % (w/v) PEG3350, 0.1 M HEPES, pH 7.5, 0.5 mM GDP, 5 mM magnesium chloride, 5 mM sodium fluoride, 0.5 mM aluminum trichloride

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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: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→34.52 Å / Num. obs: 62735 / % possible obs: 91.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.27 Å2 / CC1/2: 0.986 / Net I/σ(I): 4
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 3300 / CC1/2: 0.329 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.72 Å / SU ML: 0.2747 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.1706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 3147 5.03 %
Rwork0.1875 59467 -
obs0.1903 62614 91.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 2→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8130 0 24 618 8772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00738269
X-RAY DIFFRACTIONf_angle_d0.961211191
X-RAY DIFFRACTIONf_chiral_restr0.05561306
X-RAY DIFFRACTIONf_plane_restr0.00741428
X-RAY DIFFRACTIONf_dihedral_angle_d18.30213121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.34911480.2822821X-RAY DIFFRACTION95.71
2.03-2.060.3235990.26332090X-RAY DIFFRACTION90.75
2.07-2.10.28051120.23322294X-RAY DIFFRACTION91.9
2.1-2.140.28141540.22882837X-RAY DIFFRACTION96.89
2.14-2.180.30371550.23742873X-RAY DIFFRACTION97.11
2.18-2.230.29831570.2212844X-RAY DIFFRACTION97.21
2.23-2.270.29281010.22281893X-RAY DIFFRACTION64.24
2.28-2.330.29931380.20692835X-RAY DIFFRACTION97.28
2.33-2.390.24941550.20742904X-RAY DIFFRACTION97.61
2.39-2.450.29531410.20642889X-RAY DIFFRACTION97.87
2.45-2.520.28191410.20382891X-RAY DIFFRACTION97.68
2.52-2.60.25491530.2032907X-RAY DIFFRACTION97.89
2.6-2.70.2711070.19862104X-RAY DIFFRACTION71.18
2.7-2.810.24321560.19632904X-RAY DIFFRACTION98.2
2.81-2.930.25591620.19522858X-RAY DIFFRACTION98.34
2.93-3.090.24491340.19012914X-RAY DIFFRACTION98.39
3.09-3.280.24681560.18222918X-RAY DIFFRACTION98.56
3.28-3.530.2151340.17742483X-RAY DIFFRACTION85
3.53-3.870.22541550.16062550X-RAY DIFFRACTION89.99
3.9-4.450.191340.14712855X-RAY DIFFRACTION98.61
4.45-5.60.20481730.15382892X-RAY DIFFRACTION99.29
5.6-32.720.19571820.16542911X-RAY DIFFRACTION99.55
Refinement TLS params.Method: refined / Origin x: -2.36283833596 Å / Origin y: 0.476046599972 Å / Origin z: 8.23285665721 Å
111213212223313233
T0.138500293322 Å20.0138559627329 Å20.0281207984259 Å2-0.141311500784 Å25.88889710381E-5 Å2--0.162233023049 Å2
L0.246009747876 °20.0463840490596 °20.322775780225 °2-0.10712411768 °20.0737295783264 °2--0.638270651894 °2
S0.0261144406962 Å °-0.0447249022122 Å °-0.0295116935824 Å °0.0680293683731 Å °-0.00974153429709 Å °0.0191800737336 Å °0.109281695591 Å °-0.0118663364013 Å °-0.015025298659 Å °
Refinement TLS groupSelection details: all

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