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- PDB-9bjf: Tungstate binding protein (Tungbindin) from Eubacterium limosum i... -

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Basic information

Entry
Database: PDB / ID: 9bjf
TitleTungstate binding protein (Tungbindin) from Eubacterium limosum in apo form
ComponentsMolybdenum-pterin binding domain-containing protein
KeywordsMETAL BINDING PROTEIN / Tungsten / metal binding / metal oxyanion / hexamer
Function / homologyMolybdenum-pterin binding domain / Mop domain profile. / Transport-associated OB, type 1 / TOBE domain / molybdate ion transport / Molybdate/tungstate binding, C-terminal / Molybdenum-pterin-binding protein
Function and homology information
Biological speciesEubacterium limosum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsZhou, D. / Rose, J.P. / Chen, L. / Wang, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 136885 United States
CitationJournal: Mbio / Year: 2025
Title: Storage of the vital metal tungsten in a dominant SCFA-producing human gut microbe Eubacterium limosum and implications for other gut microbes.
Authors: Shao, N. / Zhou, D. / Schut, G.J. / Poole, F.L. / Coffey, S.B. / Donaghy, A.P. / Putumbaka, S. / Thorgersen, M.P. / Chen, L. / Rose, J. / Wang, B.-.C. / Adams, M.W.W.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 23, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdenum-pterin binding domain-containing protein
B: Molybdenum-pterin binding domain-containing protein
C: Molybdenum-pterin binding domain-containing protein
D: Molybdenum-pterin binding domain-containing protein
E: Molybdenum-pterin binding domain-containing protein
F: Molybdenum-pterin binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,11514
Polymers49,3466
Non-polymers7698
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19950 Å2
ΔGint-295 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.441, 75.441, 248.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Molybdenum-pterin binding domain-containing protein / Molybdopterin-binding protein / Tungstate binding protein / Tungbindin


Mass: 8224.404 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium limosum (bacteria) / Gene: C7955_103236, SAMN04515624_10415 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U3FVB3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.59 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.1 M Sodium malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.89→47.98 Å / Num. obs: 29099 / % possible obs: 99.1 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.067 / Rrim(I) all: 0.19 / Net I/σ(I): 9.8
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 2 / Num. unique obs: 484 / CC1/2: 0.724 / CC star: 0.916 / Rrim(I) all: 0.856

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→47.98 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3227 2942 10.11 %
Rwork0.284 --
obs0.288 29099 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 40 28 3016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012980
X-RAY DIFFRACTIONf_angle_d1.3654010
X-RAY DIFFRACTIONf_dihedral_angle_d17.1741085
X-RAY DIFFRACTIONf_chiral_restr0.07504
X-RAY DIFFRACTIONf_plane_restr0.008504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.940.4442970.4341915X-RAY DIFFRACTION70
2.94-2.990.42451210.39121029X-RAY DIFFRACTION79
2.99-3.050.44141260.35951146X-RAY DIFFRACTION87
3.05-3.110.38811370.34781164X-RAY DIFFRACTION91
3.11-3.170.4151380.36411225X-RAY DIFFRACTION93
3.17-3.240.4011440.3541246X-RAY DIFFRACTION95
3.24-3.310.3621460.33421251X-RAY DIFFRACTION97
3.31-3.40.36551410.30961274X-RAY DIFFRACTION98
3.4-3.490.39321450.32151286X-RAY DIFFRACTION99
3.49-3.590.32561530.30761327X-RAY DIFFRACTION99
3.59-3.710.37521390.29851275X-RAY DIFFRACTION100
3.71-3.840.29471430.2811311X-RAY DIFFRACTION99
3.84-3.990.32041470.27471305X-RAY DIFFRACTION99
3.99-4.170.33891420.24761292X-RAY DIFFRACTION99
4.17-4.390.28961400.24471305X-RAY DIFFRACTION99
4.4-4.670.27371500.24821310X-RAY DIFFRACTION99
4.67-5.030.25261480.25951311X-RAY DIFFRACTION100
5.03-5.530.32531390.26211280X-RAY DIFFRACTION100
5.54-6.330.2631500.29271316X-RAY DIFFRACTION100
6.34-7.970.30421490.27621295X-RAY DIFFRACTION100
7.98-47.980.25361470.21391294X-RAY DIFFRACTION99

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