[English] 日本語
Yorodumi
- PDB-9d2c: Crystal Structure of Tungbindin Treated with Proteinase K -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more