[English] 日本語
Yorodumi
- PDB-8d32: Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d32
TitleMycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to 5-deoxyadenosylrhodibalamin and PPPi
ComponentsCorrinoid adenosyltransferase
KeywordsTRANSFERASE / chaperone / B12 trafficking / rhodium
Function / homology
Function and homology information


corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / porphyrin-containing compound biosynthetic process / cobalamin biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily
Similarity search - Domain/homology
TRIPHOSPHATE / 5'-DEOXYADENOSINE / Chem-SF0 / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMascarenhas, R.N. / Ruetz, M. / Koutmos, M. / Banerjee, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1-DK45776 United States
American Heart Association19POST34370113 United States
CitationJournal: Biochemistry / Year: 2024
Title: A Noble Metal Substitution Leads to B 12 Cofactor Mimicry by a Rhodibalamin.
Authors: Ruetz, M. / Mascarenhas, R. / Widner, F. / Kieninger, C. / Koutmos, M. / Krautler, B. / Banerjee, R.
History
DepositionMay 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: 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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6516
Polymers20,7181
Non-polymers1,9325
Water57632
1
A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95218
Polymers62,1553
Non-polymers5,79615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area16820 Å2
ΔGint-113 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.618, 62.618, 266.997
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Corrinoid adenosyltransferase / Cob(II)alamin adenosyltransferase / Cob(II)yrinic acid a / c-diamide adenosyltransferase / ...Cob(II)alamin adenosyltransferase / Cob(II)yrinic acid a / c-diamide adenosyltransferase / Cobinamide/cobalamin adenosyltransferase / pduO-type ATP:cobalamin adenosyltransferase


Mass: 20718.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1354 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WP98, corrinoid adenosyltransferase

-
Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-SF0 / [5-(5,6-dimethyl-1H-benzimidazol-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl 1-{3-[3,14,19-tris(2-amino-2-oxoethyl)-8,13,18-tris(3-amino-3-oxopropyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1~2,5~.1~7,10~.1~12,15~]tricosa-5(23),6,10,12(21),15,17(20)-hexaen-4-yl-kappa~4~N~20~,N~21~,N~22~,N~23~]propanamido}propan-2-yl hydrogenato phosphate]rhodium (non-preferred name)


Mass: 1374.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89N13O14PRh / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30-32 % PEG 3350, 0.1 M bis Tris pH 6.5, 5 % glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.85→42.09 Å / Num. obs: 17763 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.152 / Net I/σ(I): 7.5
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.932 / Num. unique obs: 1062 / CC1/2: 0.607

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WH5

6wh5


Resolution: 1.85→38.049 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 894 5.05 %
Rwork0.2185 16826 -
obs0.2198 17720 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.74 Å2 / Biso mean: 39.9389 Å2 / Biso min: 18.55 Å2
Refinement stepCycle: final / Resolution: 1.85→38.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 212 32 1640
Biso mean--38.93 28.08 -
Num. residues----186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8501-1.9660.3681500.3131271799
1.966-2.11770.31761530.27172743100
2.1177-2.33080.26791510.24722778100
2.3308-2.6680.24321440.22712800100
2.668-3.36110.26821430.22362822100
3.3611-38.040.20491530.1892966100

+
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