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- PDB-9bem: Tungstate binding protein (Tungbindin) from Eubacterium limosum w... -

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Basic information

Entry
Database: PDB / ID: 9bem
TitleTungstate binding protein (Tungbindin) from Eubacterium limosum with seven Tungstates bound
ComponentsMolybdenum-pterin-binding 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 / TUNGSTATE(VI)ION / Molybdenum-pterin-binding protein
Function and homology information
Biological speciesEubacterium limosum (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.26 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 15, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,56414
Polymers44,7336
Non-polymers1,8318
Water6,990388
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.751, 74.751, 156.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11F-207-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 69)
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1(chain "D" and resid 1 through 69)
d_5ens_1(chain "E" and resid 1 through 69)
d_6ens_1chain "F"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 1 - 69 / Label seq-ID: 1 - 69

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF

NCS oper:
IDCodeMatrixVector
1given(-0.776259202745, -6.89718129094E-5, 0.63041386834), (0.00453333957061, -0.999974748783, 0.00547271667523), (0.63039757216, 0.00710612681838, 0.776239913929)62.7221864681, 39.4981261448, -22.4176937734
2given(0.797075056819, -0.486473610032, 0.357791532235), (-0.483106025297, -0.869178012169, -0.105537441148), (0.362325712748, -0.0887299831233, -0.92781844559)-3.10297238658, 73.8276198209, 114.877347601
3given(-0.378172050478, 0.462985225711, 0.801642427153), (0.310518303165, 0.879224630329, -0.361306563493), (-0.872103367518, 0.112288602258, -0.47626356796)17.6352729478, 9.20542658163, 153.548227892
4given(-0.243757496489, -0.300656920306, -0.922056234282), (-0.325137445392, -0.870380545047, 0.369761204573), (-0.913711072774, 0.389927074048, 0.114406959646)145.34434879, 31.2141501715, 109.028987777
5given(-0.385761284966, 0.312093082576, -0.868208580256), (0.49537711955, 0.863955268563, 0.0904588489215), (0.77832495813, -0.395195143859, -0.487884266832)137.89608579, -33.1812439231, 65.1235736314

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Components

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


Mass: 7455.546 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium limosum (bacteria) / Gene: B2M23_18525 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U3FVB3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: WO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20%(w/v) PEG 8000

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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: Mar 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 37361 / % possible obs: 95.3 % / Redundancy: 16.3 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.029 / Rrim(I) all: 0.126 / Net I/σ(I): 31.3
Reflection shellResolution: 2.26→2.3 Å / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.94 / Num. unique obs: 482 / CC1/2: 0.824 / CC star: 0.951 / Rpim(I) all: 0.291 / Rrim(I) all: 0.651

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data scaling
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.26→43.81 Å / SU ML: 0.2745 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5285
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2266 3617 9.68 %
Rwork0.1782 33744 -
obs0.1829 37361 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.48 Å2
Refinement stepCycle: LAST / Resolution: 2.26→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 40 388 3432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773040
X-RAY DIFFRACTIONf_angle_d1.04924089
X-RAY DIFFRACTIONf_chiral_restr0.0665517
X-RAY DIFFRACTIONf_plane_restr0.006509
X-RAY DIFFRACTIONf_dihedral_angle_d14.41651103
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.66783507525
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.668778515213
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.812452707875
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.544753134393
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.657727809435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.290.3936950.2905881X-RAY DIFFRACTION63.96
2.29-2.320.45791020.326975X-RAY DIFFRACTION71.14
2.32-2.350.24141080.23191028X-RAY DIFFRACTION73.96
2.35-2.390.251210.21091103X-RAY DIFFRACTION80.31
2.39-2.430.25521260.20651167X-RAY DIFFRACTION84.73
2.43-2.470.2921360.20841252X-RAY DIFFRACTION90.72
2.47-2.510.25071410.20511316X-RAY DIFFRACTION94.92
2.51-2.550.2561440.1861362X-RAY DIFFRACTION99.01
2.55-2.60.23841480.1951371X-RAY DIFFRACTION99.41
2.6-2.660.24341460.18691382X-RAY DIFFRACTION99.41
2.66-2.710.29271450.18771350X-RAY DIFFRACTION99.27
2.71-2.780.26861530.19211393X-RAY DIFFRACTION99.29
2.78-2.850.261430.19811363X-RAY DIFFRACTION99.67
2.85-2.920.2131510.19931354X-RAY DIFFRACTION99.34
2.92-3.010.24011500.18181388X-RAY DIFFRACTION99.81
3.01-3.110.27481440.18741388X-RAY DIFFRACTION99.48
3.11-3.220.20541470.19131364X-RAY DIFFRACTION99.6
3.22-3.350.22281490.17921367X-RAY DIFFRACTION99.8
3.35-3.50.2321440.17521363X-RAY DIFFRACTION98.88
3.5-3.680.21831440.18451344X-RAY DIFFRACTION97.45
3.68-3.910.18821510.14271373X-RAY DIFFRACTION99.67
3.91-4.220.18421390.1491354X-RAY DIFFRACTION97.07
4.22-4.640.17131470.13211375X-RAY DIFFRACTION99.74
4.64-5.310.20051460.14681380X-RAY DIFFRACTION99.74
5.31-6.690.22211490.18181381X-RAY DIFFRACTION99.93
6.69-43.810.21511480.17831370X-RAY DIFFRACTION99.48

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