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- PDB-9ba7: Crystal structure of Vibrio cholerae N150T NFeoB variant with a s... -

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Basic information

Entry
Database: PDB / ID: 9ba7
TitleCrystal structure of Vibrio cholerae N150T NFeoB variant with a single GDP molecule bound
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
GUANOSINE-5'-DIPHOSPHATE / Ferrous iron transport protein B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 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

Downloads & links

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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)59,70014
Polymers58,5032
Non-polymers1,19712
Water25214
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1508
Polymers29,2521
Non-polymers8987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5506
Polymers29,2521
Non-polymers2985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.466, 50.093, 62.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 63 or resid 69 through 260))
d_2ens_1(chain "B" and (resid 1 through 24 or resid 39 through 260))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETASPASPAA1 - 631 - 63
d_12ASNASNTHRTHRAA69 - 26069 - 260
d_21METMETGLYGLYBB1 - 241 - 24
d_22LYSLYSTHRTHRBB39 - 26039 - 260

NCS oper: (Code: givenMatrix: (0.262850066174, -0.660378435409, -0.703427441005), (0.594305929858, 0.685153169434, -0.42114795043), (0.760072565252, -0.307352332774, 0.572559376039)Vector: 14. ...NCS oper: (Code: given
Matrix: (0.262850066174, -0.660378435409, -0.703427441005), (0.594305929858, 0.685153169434, -0.42114795043), (0.760072565252, -0.307352332774, 0.572559376039)
Vector: 14.9375024711, -22.286633085, -37.1703667398)

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Components

#1: Protein Ferrous iron transport protein B


Mass: 29251.594 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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24% (w/v) PEG 3350, 0.1 M bis-Tris (pH 5.5), 30 mM magnesium chloride, 0.2 M ammonium sulfate, 25 mM Tris (pH 8), 5% (w/v) glycerol, 100 mM NaCl, 1 mM TCEP*HCl, 3 mM 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: 0.97934 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: 2.88→33.94 Å / Num. obs: 14956 / % possible obs: 99.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 79.56 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.8
Reflection shellResolution: 2.88→2.93 Å / Num. unique obs: 4319 / CC1/2: 0.33

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→33.94 Å / SU ML: 0.4365 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2216
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2682 710 4.75 %
Rwork0.2139 14230 -
obs0.2167 14940 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.16 Å2
Refinement stepCycle: LAST / Resolution: 2.88→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 35 14 3962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873990
X-RAY DIFFRACTIONf_angle_d1.15465393
X-RAY DIFFRACTIONf_chiral_restr0.0607631
X-RAY DIFFRACTIONf_plane_restr0.0078685
X-RAY DIFFRACTIONf_dihedral_angle_d17.40351505
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.29191973205 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.10.37781550.29882786X-RAY DIFFRACTION99.59
3.1-3.410.31851220.2652803X-RAY DIFFRACTION99.66
3.41-3.910.29231440.22232806X-RAY DIFFRACTION98.79
3.91-4.920.24341390.19182848X-RAY DIFFRACTION99.63
4.92-33.940.24381500.19782987X-RAY DIFFRACTION98.96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.70559787212-0.509069272434-0.7899901134783.61715138225-0.5584749487915.45134774651-0.025089542582-0.7995839268050.0281540351410.5156972769540.3751687513260.0563528207608-0.1381868828120.383740475926-0.3427676508170.5910684028020.08360537505490.05599470614980.786033831205-0.007787467104060.36659513708455.4292.08717.504
20.9789919478480.102449905451.262597089310.2653447752860.1185455395261.62891954636-0.476725905769-0.359576606113-0.02392998358580.3714185877060.890291745007-0.2158962839980.237263851859-0.309376280144-0.4140820653641.381354678360.4156425013090.1900068223551.785060617080.2374590425761.1638576114249.1665.95914.875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:259 )A1 - 259
2X-RAY DIFFRACTION2( CHAIN A AND RESID 302:305 ) OR ( CHAIN B AND RESID 301:302 )A302 - 305
3X-RAY DIFFRACTION2( CHAIN A AND RESID 302:305 ) OR ( CHAIN B AND RESID 301:302 )B301 - 302

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