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

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Basic information

Entry
Database: PDB / ID: 9bed
TitleTungstate binding protein (Tungbindin) from Eubacterium limosum with eight molybdates bound
ComponentsMolybdenum-pterin-binding protein
KeywordsMETAL BINDING PROTEIN / molybdate / 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 / MOLYBDATE ION / Molybdenum-pterin-binding protein
Function and homology information
Biological speciesEubacterium limosum (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.02 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)47,42414
Polymers46,1456
Non-polymers1,2808
Water8,827490
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.713, 74.713, 156.010
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
11D-275-

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_1chain "D"
d_5ens_1(chain "E" and resid 1 through 69)
d_6ens_1(chain "F" and resid 1 through 69)

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(-0.783248313136, 0.00278932905982, 0.621702742164), (-0.000820705732924, -0.999993702954, 0.00345260679876), (0.621708457729, 0.00219401344638, 0.783245670204)-3.10835060041, 114.573834115, 0.867840901343
2given(-0.380942221549, 0.317438291581, -0.868398500044), (0.498794513208, 0.861379975261, 0.0960654558779), (0.778515932679, -0.396557018924, -0.486472479497)73.5805725992, -10.0273830833, 108.612008976
3given(0.781349876379, -0.502750888444, 0.369775492498), (-0.502556248936, -0.858163266747, -0.104847624015), (0.37003998073, -0.103910306396, -0.923186363031)7.91817391987, 125.303131801, 131.514389736
4given(-0.239342856739, -0.320634102112, -0.916465367317), (-0.328066791892, -0.861679483473, 0.387144220957), (-0.913831044004, 0.393322056749, 0.101047427917)110.36594788, 87.3285319974, 60.7252223831
5given(-0.373619086331, 0.483817391001, 0.791409824613), (0.320780793009, 0.867946363982, -0.379168553664), (-0.870349620075, 0.112204462549, -0.479480653852)-51.8253437892, 26.7746985952, 116.367171532

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Components

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


Mass: 7690.808 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium limosum (bacteria) / Gene: B2M23_18525, C7955_103236, SAMN04515624_10415 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U3FVB3
#2: Chemical
ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: MoO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Magnesium acetate, 0.1 M Sodium cacodylate pH 6.5, 15%(w/v) PEG 6000

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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 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→37.36 Å / Num. obs: 54278 / % possible obs: 97.68 % / Redundancy: 18.9 % / Biso Wilson estimate: 23.05 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.023 / Net I/σ(I): 47
Reflection shellResolution: 2.02→2.05 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.93 / Num. unique obs: 916 / CC1/2: 0.911 / Rpim(I) all: 0.149 / Rrim(I) all: 0.337

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data scaling
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→37.36 Å / SU ML: 0.1857 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4054
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2048 3704 6.82 %
Rwork0.1506 50574 -
obs0.1543 54278 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.43 Å2
Refinement stepCycle: LAST / Resolution: 2.02→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 40 490 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01073059
X-RAY DIFFRACTIONf_angle_d1.21614116
X-RAY DIFFRACTIONf_chiral_restr0.0676512
X-RAY DIFFRACTIONf_plane_restr0.0071513
X-RAY DIFFRACTIONf_dihedral_angle_d12.53881110
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.324264590359
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.626396161575
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.687516338397
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.500586125901
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.569492190544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.040.25381100.20311527X-RAY DIFFRACTION78.03
2.04-2.070.26821220.18921763X-RAY DIFFRACTION85.88
2.07-2.10.25871330.1861796X-RAY DIFFRACTION92.47
2.1-2.130.24211380.1751942X-RAY DIFFRACTION95.28
2.13-2.170.24041420.16871901X-RAY DIFFRACTION97.33
2.17-2.20.22171440.16971994X-RAY DIFFRACTION98.39
2.2-2.240.23091430.15861948X-RAY DIFFRACTION98.77
2.24-2.280.23811470.15791974X-RAY DIFFRACTION99.58
2.28-2.320.25211450.17641982X-RAY DIFFRACTION99.16
2.32-2.370.23411460.16031969X-RAY DIFFRACTION99.86
2.37-2.420.21541520.15011989X-RAY DIFFRACTION99.54
2.42-2.480.20491490.16461993X-RAY DIFFRACTION99.67
2.48-2.540.20031480.1451969X-RAY DIFFRACTION99.3
2.54-2.610.2171450.1591962X-RAY DIFFRACTION99.48
2.61-2.690.26011460.14561985X-RAY DIFFRACTION99.72
2.69-2.770.20411470.16342003X-RAY DIFFRACTION99.72
2.77-2.870.19261440.15421983X-RAY DIFFRACTION99.58
2.87-2.990.24791420.15661985X-RAY DIFFRACTION99.81
2.99-3.120.2411450.14711982X-RAY DIFFRACTION99.67
3.12-3.290.20991460.15671975X-RAY DIFFRACTION99.72
3.29-3.490.17581390.14071997X-RAY DIFFRACTION99.81
3.49-3.760.17941480.13292002X-RAY DIFFRACTION99.86
3.76-4.140.18071440.12341980X-RAY DIFFRACTION99.62
4.14-4.740.15661450.11631989X-RAY DIFFRACTION99.95
4.74-5.970.16691460.14371986X-RAY DIFFRACTION99.86
5.97-37.360.19761480.1771998X-RAY DIFFRACTION99.91

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