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- PDB-9ps9: High-resolution crystal structure of Vibrio cholerae NFeoB in the... -

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Basic information

Entry
Database: PDB / ID: 9ps9
TitleHigh-resolution crystal structure of Vibrio cholerae NFeoB in the apo form in orthorhombic space group
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
TRIFLUOROETHANOL / Ferrous iron transport protein B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)120,99641
Polymers117,3984
Non-polymers3,59837
Water15,277848
1
A: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,31811
Polymers29,3501
Non-polymers96910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,23410
Polymers29,3501
Non-polymers8849
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1309
Polymers29,3501
Non-polymers7808
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ferrous iron transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,31411
Polymers29,3501
Non-polymers96510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.483, 101.106, 301.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ETF / TRIFLUOROETHANOL


Mass: 100.040 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H3F3O
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.4 M lithium sulfate, 0.1 M HEPES sodium, pH 7.2, 2 % (v/v) trifluoroethane

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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: 0.97935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.85→43.53 Å / Num. obs: 125249 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.997 / Net I/σ(I): 10.2
Reflection shellResolution: 1.85→1.88 Å / Num. unique obs: 6208 / CC1/2: 0.373

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Processing

Software
NameVersionClassification
REFMAC4.4.7refinement
AutoProcessdata reduction
AutoProcessdata scaling
AutoProcessphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→43.53 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 7.065 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20728 6463 5.2 %RANDOM
Rwork0.17599 ---
obs0.17761 118785 99.94 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.347 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å2-0 Å2
2---2.57 Å2-0 Å2
3---3.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8118 0 208 848 9174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0178401
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168184
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.82211353
X-RAY DIFFRACTIONr_angle_other_deg0.5071.56318769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845.3131085
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.725101525
X-RAY DIFFRACTIONr_chiral_restr0.0730.21342
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021873
X-RAY DIFFRACTIONr_mcbond_it3.681.2324092
X-RAY DIFFRACTIONr_mcbond_other3.6781.2324092
X-RAY DIFFRACTIONr_mcangle_it4.742.1815101
X-RAY DIFFRACTIONr_mcangle_other4.742.1815102
X-RAY DIFFRACTIONr_scbond_it9.7532.2134309
X-RAY DIFFRACTIONr_scbond_other9.262.1574254
X-RAY DIFFRACTIONr_scangle_other11.5723.4966169
X-RAY DIFFRACTIONr_long_range_B_refined12.69716.019369
X-RAY DIFFRACTIONr_long_range_B_other12.73214.059124
LS refinement shellResolution: 1.852→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 420 -
Rwork0.329 8718 -
obs--99.87 %
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)
11.11110.1801-0.39242.44420.76771.09440.1119-0.02650.0858-0.069-0.04730.0531-0.0976-0.0631-0.06470.1711-0.05230.08240.2779-0.02080.045211.46518.23255.263
20.9430.1205-0.17922.61610.190.67560.067-0.1185-0.12760.0432-0.0804-0.04230.00020.08430.01340.1391-0.0550.0520.2874-0.03570.049548.41830.73950.831
32.823-0.0398-0.1771.14230.10590.5704-0.0638-0.01230.0608-0.04890.04240.1701-0.05-0.00530.02140.2106-0.0480.05510.1798-0.05170.058629.78248.44824.784
42.17370.2078-0.66941.02450.40831.06130.0087-0.0925-0.0067-0.00540.0713-0.0650.05980.0961-0.080.2078-0.04670.01610.2112-0.06910.027719.02310.96720.167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 261
2X-RAY DIFFRACTION2B1 - 261
3X-RAY DIFFRACTION3C1 - 261
4X-RAY DIFFRACTION4D1 - 261

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