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- PDB-9ba6: High-resolution crystal structure of Vibrio cholerae NFeoB in the... -

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Basic information

Entry
Database: PDB / ID: 9ba6
TitleHigh-resolution crystal structure of Vibrio cholerae NFeoB in the apo form
ComponentsFerrous iron transport protein B
KeywordsTRANSPORT PROTEIN / iron / transport / Feo / G-protein
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
Ferrous iron transport protein B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsLee, M. / 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: J.Biol.Chem. / Year: 2024
Title: Structural determinants of Vibrio cholerae FeoB nucleotide promiscuity.
Authors: Lee, M. / Magante, K. / Gomez-Garzon, C. / Payne, S.M. / Smith, A.T.
History
DepositionApr 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,41511
Polymers58,6992
Non-polymers7169
Water1,65792
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7536
Polymers29,3501
Non-polymers4045
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)29,6615
Polymers29,3501
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.962, 73.442, 63.027
Angle α, β, γ (deg.)90.000, 94.250, 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 Ferrous iron transport protein B


Mass: 29349.588 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) PEG 2000, 0.1 M Tris (pH 8.0), 5% (v/v) glycerol, 100 mM NaCl, 1 mM TCEP-HCl, 3 mM ADP

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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: Mar 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.38→43.41 Å / Num. obs: 19722 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.992 / Net I/σ(I): 11.4
Reflection shellResolution: 2.38→2.42 Å / Num. unique obs: 3313 / CC1/2: 0.521

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→39.46 Å / SU ML: 0.3319 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2665 897 4.55 %
Rwork0.205 18797 -
obs0.2078 19694 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.1 Å2
Refinement stepCycle: LAST / Resolution: 2.38→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3954 0 44 92 4090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00934053
X-RAY DIFFRACTIONf_angle_d1.70145461
X-RAY DIFFRACTIONf_chiral_restr0.0864640
X-RAY DIFFRACTIONf_plane_restr0.014703
X-RAY DIFFRACTIONf_dihedral_angle_d16.18861541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.530.33221940.26653074X-RAY DIFFRACTION99.33
2.53-2.730.32231360.25243088X-RAY DIFFRACTION99.54
2.73-30.28691270.22093162X-RAY DIFFRACTION99.73
3-3.440.26311420.19793128X-RAY DIFFRACTION99.97
3.44-4.330.25691590.18593137X-RAY DIFFRACTION100
4.33-39.460.23951390.19433208X-RAY DIFFRACTION99.91

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