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

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Basic information

Entry
Database: PDB / ID: 9bel
TitleTungstate binding protein (Tungbindin) from Eubacterium limosum with five Tungstates bound
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 / TUNGSTATE(VI)ION / Molybdenum-pterin-binding protein
Function and homology information
Biological speciesEubacterium limosum (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.68 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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 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)50,97015
Polymers49,3466
Non-polymers1,6239
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.306, 74.306, 148.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 69)
d_2ens_1(chain "B" and resid 1 through 69)
d_3ens_1(chain "C" and resid 1 through 69)
d_4ens_1chain "D"
d_5ens_1chain "E"
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(-0.864013701785, 0.00115847657775, 0.50346696124), (0.0077848205944, -0.999847062617, 0.0156603941666), (0.50340810452, 0.0174501951037, 0.863872543258)-25.120086172, 38.4171220711, 6.37002340609
2given(-0.131692489842, -0.354599150773, -0.925697861287), (-0.404365887267, -0.833388381574, 0.376765224872), (-0.905066471224, 0.423937787569, -0.0336368092513)-16.4640096954, 31.821383621, -29.0081368956
3given(-0.35427633082, 0.308306375407, -0.882856421115), (0.522702980947, 0.848122871688, 0.0864244654587), (0.775415936856, -0.430853540549, -0.461622520536)-32.5072588871, 11.5433628225, 10.2478742006
4given(-0.372269808657, 0.519733808893, 0.768955107569), (0.326510555603, 0.848880528689, -0.415683419313), (-0.868795745064, 0.0963255724371, -0.485711166695)-25.4774116748, 4.86635595877, -25.1094412132
5given(0.721794515435, -0.4979623781, 0.480672599058), (-0.467632199983, -0.862883467352, -0.191708756474), (0.510228187213, -0.0864036559854, -0.855687796574)8.68343172318, 27.0824465821, -3.05718609161

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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-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: WO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium citrate tribasic pH 7.0 20% w/v Polyethylene glycol 3,350

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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: Feb 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.68→42.88 Å / Num. obs: 21946 / % possible obs: 98.81 % / Redundancy: 22.9 % / Biso Wilson estimate: 47.72 Å2 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.036 / Rrim(I) all: 0.177 / Net I/σ(I): 31.75
Reflection shellResolution: 2.683→2.73 Å / Rmerge(I) obs: 1.018 / Num. unique obs: 724 / CC1/2: 0.898 / Rpim(I) all: 0.248 / Rrim(I) all: 1.049

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.68→42.88 Å / SU ML: 0.3657 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.0235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2653 2215 10.09 %
Rwork0.2025 19731 -
obs0.209 21946 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.54 Å2
Refinement stepCycle: LAST / Resolution: 2.68→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 45 126 3161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093028
X-RAY DIFFRACTIONf_angle_d1.24984072
X-RAY DIFFRACTIONf_chiral_restr0.0699514
X-RAY DIFFRACTIONf_plane_restr0.0081507
X-RAY DIFFRACTIONf_dihedral_angle_d16.4071100
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.742918298855
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.935066287238
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.621684419473
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.775045529547
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.786183559217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.740.36271340.29481202X-RAY DIFFRACTION97.66
2.74-2.810.36711320.28431240X-RAY DIFFRACTION98.56
2.81-2.880.35361360.27251225X-RAY DIFFRACTION98.62
2.88-2.950.36981360.26111263X-RAY DIFFRACTION98.8
2.95-3.040.30361380.24041205X-RAY DIFFRACTION98.82
3.04-3.140.29181370.23831264X-RAY DIFFRACTION99.08
3.14-3.250.34751360.22631238X-RAY DIFFRACTION99.64
3.25-3.380.31141430.24381242X-RAY DIFFRACTION98.72
3.38-3.530.28871370.20961234X-RAY DIFFRACTION98.35
3.53-3.720.32251420.22751196X-RAY DIFFRACTION97.81
3.72-3.950.33221390.19761248X-RAY DIFFRACTION98.93
3.95-4.260.21581390.17561216X-RAY DIFFRACTION97.48
4.26-4.690.18911390.14961216X-RAY DIFFRACTION99.71
4.69-5.360.20131440.1721265X-RAY DIFFRACTION99.72
5.37-6.750.2241460.18031241X-RAY DIFFRACTION99.57
6.75-42.880.21370.1721236X-RAY DIFFRACTION99.42

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