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- PDB-9d8d: Crystal structure of Vibrio cholerae NFeoB in the GMPPCP-bound form -

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Basic information

Entry
Database: PDB / ID: 9d8d
TitleCrystal structure of Vibrio cholerae NFeoB in the GMPPCP-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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Ferrous iron transport protein B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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: Crystal structure of Vibrio cholerae NFeoB in the GMPPCP-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)119,10711
Polymers116,8824
Non-polymers2,2267
Water3,027168
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8343
Polymers29,2201
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7422
Polymers29,2201
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7663
Polymers29,2201
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7663
Polymers29,2201
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.977, 59.666, 89.432
Angle α, β, γ (deg.)93.59, 92.61, 113.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ferrous iron transport protein B


Mass: 29220.473 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-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 26 % (w/v) PEG 4000, 0.2 M ammonium acetate, 0.1 M bicine (pH 8.4), 0.010 M magnesium chloride, 0.003 M GMPPCP

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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: 0.97936 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: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.11→88.99 Å / Num. obs: 57054 / % possible obs: 97.6 % / Redundancy: 1.8 % / CC1/2: 0.99 / Net I/σ(I): 9.4
Reflection shellResolution: 2.11→2.15 Å / Num. unique obs: 5091 / CC1/2: 0.557

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Processing

Software
NameVersionClassification
PHENIX1.21.1refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→31.81 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 2778 4.89 %
Rwork0.1957 --
obs0.1981 56826 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→31.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7890 0 136 168 8194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1
X-RAY DIFFRACTIONf_dihedral_angle_d21.7793152
X-RAY DIFFRACTIONf_chiral_restr0.0521287
X-RAY DIFFRACTIONf_plane_restr0.0071401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.150.35291280.33542540X-RAY DIFFRACTION90
2.15-2.190.3171300.30962587X-RAY DIFFRACTION95
2.19-2.230.31421550.28892723X-RAY DIFFRACTION96
2.23-2.270.33961220.28532663X-RAY DIFFRACTION96
2.27-2.320.28231420.26472720X-RAY DIFFRACTION97
2.32-2.380.33431410.25762690X-RAY DIFFRACTION97
2.38-2.440.31881470.25032687X-RAY DIFFRACTION97
2.44-2.50.25071460.23912692X-RAY DIFFRACTION97
2.5-2.580.29761520.22452698X-RAY DIFFRACTION98
2.58-2.660.2921490.20982694X-RAY DIFFRACTION98
2.66-2.750.23351350.21082706X-RAY DIFFRACTION97
2.75-2.860.28611410.21162769X-RAY DIFFRACTION98
2.86-2.990.28071640.20372705X-RAY DIFFRACTION98
2.99-3.150.27831350.19452713X-RAY DIFFRACTION98
3.15-3.350.30111340.19052735X-RAY DIFFRACTION98
3.35-3.610.23081350.18782707X-RAY DIFFRACTION98
3.61-3.970.19231120.17772755X-RAY DIFFRACTION98
3.97-4.540.19081410.16152775X-RAY DIFFRACTION99
4.54-5.720.24151410.18072749X-RAY DIFFRACTION99
5.72-31.810.22321280.17912740X-RAY DIFFRACTION98
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)
12.5492-0.0745-0.42393.2287-0.72671.6027-0.02410.08430.1152-0.192-0.01090.03720.01370.03460.00110.283-0.0109-0.00230.3425-0.04520.3027-11.529332.6943-54.6644
21.74040.5979-1.19174.6147-0.61482.8511-0.002-0.1840.00480.3383-0.01540.44980.355-0.10940.00820.45870.03130.00320.45810.03450.4655-12.19162.2675-19.711
32.36340.59170.28122.7920.33792.2361-0.0034-0.13580.03240.0364-0.11760.02350.00070.2079-0.00050.3375-0.03090.00070.385-0.00280.354-33.02298.4035-63.1972
41.96720.10390.50612.05150.21221.95620.10710.02140.303-0.0135-0.06030.1692-0.21780.0540.00010.57610.0116-0.00070.48350.05550.45342.953429.5288-8.186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:260)
2X-RAY DIFFRACTION2(chain B and resseq 1:65) or (chain B and resseq 70:260)
3X-RAY DIFFRACTION3(chain C and resseq 1:25) or (chain C and resseq 39:63) or (chain C and resseq 70:260)
4X-RAY DIFFRACTION4(chain D and resseq 1:25) or (chain D and resseq 39:63) or (chain D and resseq 71:260)

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