[English] 日本語
Yorodumi
- PDB-8jbs: B12-binding domain from Chloracidobacterium thermophilum MerR fam... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jbs
TitleB12-binding domain from Chloracidobacterium thermophilum MerR family protein, dark state
ComponentsPutative cobalamin binding protein
KeywordsTRANSCRIPTION / B12-dependent transcription regulators from the MerR superfamily
Function / homology5'-DEOXYADENOSINE / COBALAMIN
Function and homology information
Biological speciesChloracidobacterium thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, S. / Yu, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/S030336/1 United Kingdom
CitationJournal: Febs J. / Year: 2025
Title: SignatureFinder enables sequence mining to identify cobalamin-dependent photoreceptor proteins.
Authors: Yu, Y. / Jeffreys, L.N. / Poddar, H. / Hill, A. / Johannissen, L. / Dai, F. / Sakuma, M. / Leys, D. / Heyes, D.J. / Zhang, S. / Scrutton, N.S.
History
DepositionMay 9, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative cobalamin binding protein
B: Putative cobalamin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4136
Polymers72,2502
Non-polymers3,1634
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-9 kcal/mol
Surface area20820 Å2
MethodPISA
2
A: Putative cobalamin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7073
Polymers36,1251
Non-polymers1,5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-12 kcal/mol
Surface area11180 Å2
MethodPISA
3
B: Putative cobalamin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7073
Polymers36,1251
Non-polymers1,5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-10 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.218, 125.218, 73.088
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Putative cobalamin binding protein


Mass: 36124.918 Da / Num. of mol.: 2 / Fragment: B12-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloracidobacterium thermophilum (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Amino acids, 0.1 M Buffer System 3 (Bicine and Tris) pH 8.5, 50% v/v Precipitant Mix 3 (Glycerol and Poly(ethylene glycol) 4000)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→108.442 Å / Num. obs: 29650 / % possible obs: 100 % / Redundancy: 20.6 % / CC1/2: 1 / Rrim(I) all: 0.163 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 19.5 % / Rmerge(I) obs: 2.659 / Mean I/σ(I) obs: 0.62 / Num. unique obs: 2912 / CC1/2: 0.538 / % possible all: 98.91

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→108.44 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.602 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23609 1503 5.1 %RANDOM
Rwork0.18531 ---
obs0.18791 28126 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.044 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å2-1.12 Å2-0 Å2
2---2.25 Å2-0 Å2
3---7.29 Å2
Refinement stepCycle: 1 / Resolution: 2.3→108.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 0 37 3825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123902
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153653
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.9055378
X-RAY DIFFRACTIONr_angle_other_deg0.6091.8058314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6595447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.541542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4510565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024701
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02985
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0555.811794
X-RAY DIFFRACTIONr_mcbond_other5.0445.8111794
X-RAY DIFFRACTIONr_mcangle_it6.93310.4292239
X-RAY DIFFRACTIONr_mcangle_other6.93310.4332240
X-RAY DIFFRACTIONr_scbond_it5.796.0992108
X-RAY DIFFRACTIONr_scbond_other5.7896.0982109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.29310.9743140
X-RAY DIFFRACTIONr_long_range_B_refined9.87456.664317
X-RAY DIFFRACTIONr_long_range_B_other9.87656.534315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 83 -
Rwork0.362 2069 -
obs--98.9 %

+
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://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