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- PDB-9d2c: Crystal Structure of Tungbindin Treated with Proteinase K -

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Basic information

Entry
Database: PDB / ID: 9d2c
TitleCrystal Structure of Tungbindin Treated with Proteinase K
ComponentsMolybdenum-pterin binding domain-containing protein
KeywordsTRANSPORT PROTEIN / tungstate binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionAug 8, 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 16, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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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
H: Molybdenum-pterin binding domain-containing protein
I: Molybdenum-pterin binding domain-containing protein
J: Molybdenum-pterin binding domain-containing protein
K: Molybdenum-pterin binding domain-containing protein
L: Molybdenum-pterin binding domain-containing protein
M: Molybdenum-pterin binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,25228
Polymers98,69312
Non-polymers2,55916
Water5,945330
1
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)50,62614
Polymers49,3466
Non-polymers1,2808
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Molybdenum-pterin binding domain-containing protein
I: Molybdenum-pterin binding domain-containing protein
J: Molybdenum-pterin binding domain-containing protein
K: Molybdenum-pterin binding domain-containing protein
L: Molybdenum-pterin binding domain-containing protein
M: Molybdenum-pterin binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,62614
Polymers49,3466
Non-polymers1,2808
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.901, 76.696, 103.119
Angle α, β, γ (deg.)90.000, 102.318, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name N or name...
d_2ens_1(chain "B" and ((resid 1 and (name N or name...
d_3ens_1(chain "C" and ((resid 1 and (name N or name...
d_4ens_1(chain "D" and ((resid 1 and (name N or name...
d_5ens_1(chain "E" and ((resid 1 and (name N or name...
d_6ens_1(chain "F" and ((resid 1 and (name N or name...
d_7ens_1(chain "H" and ((resid 1 and (name N or name...
d_8ens_1(chain "I" and ((resid 1 and (name N or name...
d_9ens_1(chain "J" and ((resid 1 and (name N or name...
d_10ens_1(chain "K" and ((resid 1 and (name N or name...
d_11ens_1(chain "L" and ((resid 1 and (name N or name...
d_12ens_1(chain "M" and ((resid 1 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETASPASPAA1 - 691 - 69
d_12MOOMOOMOOMOOAM101
d_21METMETASPASPBB1 - 691 - 69
d_22MOOMOOMOOMOOBO102
d_31METMETASPASPCC1 - 691 - 69
d_32MOOMOOMOOMOOCQ102
d_41METMETASPASPDD1 - 691 - 69
d_42MOOMOOMOOMOODR101
d_51METMETASPASPEE1 - 691 - 69
d_52MOOMOOMOOMOOES101
d_61METMETASPASPFF1 - 691 - 69
d_62MOOMOOMOOMOOFT101
d_71METMETASPASPHG1 - 691 - 69
d_72MOOMOOMOOMOOHU101
d_81METMETASPASPIH1 - 691 - 69
d_82MOOMOOMOOMOOIW101
d_91METMETASPASPJI1 - 691 - 69
d_92MOOMOOMOOMOOJY101
d_101METMETASPASPKJ1 - 691 - 69
d_102MOOMOOMOOMOOIX102
d_111METMETASPASPLK1 - 691 - 69
d_112MOOMOOMOOMOOLAA101
d_121METMETASPASPML1 - 691 - 69
d_122MOOMOOMOOMOOHV102

NCS oper:
IDCodeMatrixVector
1given(-0.497951610824, -0.235834774449, -0.83452151107), (-0.236292875093, -0.889002427343, 0.392224886206), (-0.834391916582, 0.392500501069, 0.38695411382)14.480463656, -16.8265540485, 13.6994110247
2given(-0.501635954417, -0.23379121213, -0.832888370892), (0.234032535742, 0.890211238923, -0.390835927608), (0.832820593796, -0.390980330996, -0.391847214261)14.6122045919, -4.40727921686, -13.7082551813
3given(-0.479812261228, 0.212980822124, 0.85112828844), (0.239946043684, -0.901252713187, 0.360790026321), (0.843923035647, 0.377336343836, 0.381328196603)19.3177914933, -23.0145267037, -5.85931794224
4given(0.999985544966, -0.00532599384866, -0.000737324698949), (-0.00532645811172, -0.999985616414, -0.000629133705795), (-0.000733963331329, 0.00063305194077, -0.999999530271)-0.0766934277013, -21.1781243159, -0.0242595008193
5given(-0.481051509037, 0.213198163175, 0.850374028808), (-0.239748213737, 0.901013539918, -0.361518180587), (-0.843273526006, -0.377784520731, -0.382320044247)19.3253686898, 1.83397326596, 5.8334463666
6given(0.901190716578, 0.000899904572504, 0.433421829776), (-0.00110413179819, -0.999989833117, 0.00437201963424), (0.433421357627, -0.00441857833136, -0.901180560664)11.0179343875, -2.30677690681, -50.4903451611
7given(-0.814226800952, -0.0450905404968, -0.578793192573), (0.221233254425, 0.897650890935, -0.381154463624), (0.536740685758, -0.438394481218, -0.720915886279)30.2117131191, 15.2286753701, -56.3012178304
8given(-0.0938680612375, -0.378240493095, -0.920935891614), (-0.219902102957, -0.894296692661, 0.389713344153), (-0.970995289481, 0.239097375309, 0.000770016856047)18.481878328, 1.42801098087, -31.6857900593
9given(-0.0849814964555, 0.376838967737, 0.922372233784), (-0.231974343344, 0.892799944098, -0.386129724119), (-0.96900260541, -0.246780575032, 0.0115454968022)26.4986630511, 19.9481328705, -36.8500352574
10given(0.900041219344, 0.00980413026536, -0.435694482994), (-0.0095234119204, 0.999950652049, 0.00282808991749), (0.435700709326, 0.00160390053524, 0.900090172925)11.1038801491, 19.13288912, -50.4315423394
11given(-0.806112751676, 0.0421679663748, 0.59025765069), (0.233869355709, -0.89355462957, 0.383230020267), (0.543587487021, 0.446969782631, 0.710443986088)31.2750030535, -3.32132496452, -46.8872683087

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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.: 12
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-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: MoO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES pH 7.0 15% PEG 4000 0.1M MgCl2

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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: Jun 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→43.95 Å / Num. obs: 53472 / % possible obs: 88.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 34.38 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.55
Reflection shellResolution: 2.38→2.41 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.42 / Num. unique obs: 403

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→43.95 Å / SU ML: 0.2985 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 3625 6.78 %
Rwork0.1828 49847 -
obs0.1862 53472 81.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.02 Å2
Refinement stepCycle: LAST / Resolution: 2.38→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 80 330 6452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096118
X-RAY DIFFRACTIONf_angle_d1.17668232
X-RAY DIFFRACTIONf_chiral_restr0.0631024
X-RAY DIFFRACTIONf_plane_restr0.00731026
X-RAY DIFFRACTIONf_dihedral_angle_d13.70042220
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.72083880489
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS2.73920091775
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.685026563723
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.741649292684
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.709879316897
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.532060245249
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.58239514226
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS0.535983443341
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS2.71505646111
ens_1d_11AAX-RAY DIFFRACTIONTorsion NCS0.714480511511
ens_1d_12AAX-RAY DIFFRACTIONTorsion NCS2.76686279089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.410.3813410.2328426X-RAY DIFFRACTION18.76
2.41-2.450.3463460.2342677X-RAY DIFFRACTION28.55
2.45-2.480.3569700.2355819X-RAY DIFFRACTION34.39
2.48-2.520.279660.2467972X-RAY DIFFRACTION41.06
2.52-2.560.2845820.20471143X-RAY DIFFRACTION49
2.56-2.60.2783800.2181383X-RAY DIFFRACTION58.06
2.6-2.640.29541310.22851532X-RAY DIFFRACTION65.06
2.64-2.690.30431460.23141797X-RAY DIFFRACTION77.78
2.69-2.740.34251370.22432175X-RAY DIFFRACTION89.34
2.74-2.80.28951540.21492171X-RAY DIFFRACTION93.98
2.8-2.860.24291540.2022358X-RAY DIFFRACTION96.17
2.86-2.930.31231840.19462196X-RAY DIFFRACTION96.43
2.93-30.26351420.18692267X-RAY DIFFRACTION96.59
3-3.080.26891820.18422299X-RAY DIFFRACTION97.03
3.08-3.170.22831610.20512288X-RAY DIFFRACTION97.38
3.17-3.270.25641650.21322310X-RAY DIFFRACTION97.52
3.27-3.390.27591730.19742289X-RAY DIFFRACTION97.16
3.39-3.530.24881620.21642278X-RAY DIFFRACTION95.57
3.53-3.690.26491580.20412282X-RAY DIFFRACTION96.83
3.69-3.880.23971640.16462323X-RAY DIFFRACTION98.22
3.88-4.120.22131610.15962258X-RAY DIFFRACTION96.8
4.12-4.440.16351860.13512317X-RAY DIFFRACTION98.66
4.44-4.890.17281610.13512345X-RAY DIFFRACTION98.97
4.89-5.60.18491670.14942342X-RAY DIFFRACTION98.9
5.6-7.050.21051810.18552331X-RAY DIFFRACTION98.55
7.05-43.950.1951710.18512269X-RAY DIFFRACTION96.83

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