[English] 日本語
Yorodumi
- PDB-6wh5: Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wh5
TitleMycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to cob(II)alamin and PPPi
ComponentsCorrinoid adenosyltransferase
KeywordsTRANSFERASE / chaperone / B12 trafficking
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 / COBALAMIN / : / Corrinoid adenosyltransferase / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.866 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: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B 12 .
Authors: Mascarenhas, R. / Ruetz, M. / McDevitt, L. / Koutmos, M. / Banerjee, R.
History
DepositionApr 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.classification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Corrinoid adenosyltransferase
B: Corrinoid adenosyltransferase
C: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95715
Polymers63,0023
Non-polymers4,95512
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-127 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.428, 62.678, 103.071
Angle α, β, γ (deg.)90.000, 119.040, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 20 or resid 22...
21(chain B and (resid 3 through 20 or resid 22...
31(chain C and (resid 3 through 20 or resid 22...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEU(chain A and (resid 3 through 20 or resid 22...AA3 - 206 - 23
12ASPASPASPASP(chain A and (resid 3 through 20 or resid 22...AA2225
13SERSERSERSER(chain A and (resid 3 through 20 or resid 22...AA2427
14GLUGLUGLUGLU(chain A and (resid 3 through 20 or resid 22...AA8386
15VALVALGLYGLY(chain A and (resid 3 through 20 or resid 22...AA3 - 1886 - 191
16VALVALGLYGLY(chain A and (resid 3 through 20 or resid 22...AA3 - 1886 - 191
17VALVALGLYGLY(chain A and (resid 3 through 20 or resid 22...AA3 - 1886 - 191
18VALVALGLYGLY(chain A and (resid 3 through 20 or resid 22...AA3 - 1886 - 191
21VALVALLEULEU(chain B and (resid 3 through 20 or resid 22...BB3 - 206 - 23
22ASPASPASPASP(chain B and (resid 3 through 20 or resid 22...BB2225
23SERSERSERSER(chain B and (resid 3 through 20 or resid 22...BB2427
24GLUGLUGLUGLU(chain B and (resid 3 through 20 or resid 22...BB8386
25VALVALGLYGLY(chain B and (resid 3 through 20 or resid 22...BB3 - 1886 - 191
26VALVALGLYGLY(chain B and (resid 3 through 20 or resid 22...BB3 - 1886 - 191
27VALVALGLYGLY(chain B and (resid 3 through 20 or resid 22...BB3 - 1886 - 191
28VALVALGLYGLY(chain B and (resid 3 through 20 or resid 22...BB3 - 1886 - 191
31VALVALLEULEU(chain C and (resid 3 through 20 or resid 22...CC3 - 206 - 23
32ASPASPASPASP(chain C and (resid 3 through 20 or resid 22...CC2225
33SERSERSERSER(chain C and (resid 3 through 20 or resid 22...CC2427
34LYSLYSHISHIS(chain C and (resid 3 through 20 or resid 22...CC86 - 8789 - 90
35VALVALGLYGLY(chain C and (resid 3 through 20 or resid 22...CC3 - 1886 - 191
36VALVALGLYGLY(chain C and (resid 3 through 20 or resid 22...CC3 - 1886 - 191
37VALVALGLYGLY(chain C and (resid 3 through 20 or resid 22...CC3 - 1886 - 191
38VALVALGLYGLY(chain C and (resid 3 through 20 or resid 22...CC3 - 1886 - 191

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Corrinoid adenosyltransferase


Mass: 21000.648 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: E5M05_13560, ERS023446_03354, ERS027651_01619, FCN16_21305, SAMEA2682864_01680, SAMEA2683035_01578
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045JVI3, UniProt: P9WP99*PLUS, corrinoid adenosyltransferase

-
Non-polymers , 5 types, 218 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% 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: 1.127 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.866→54.156 Å / Num. obs: 46346 / % possible obs: 91.9 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.2
Reflection shellResolution: 1.866→1.898 Å / Rmerge(I) obs: 0.745 / Num. unique obs: 12179 / CC1/2: 0.818

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G2D

2g2d


Resolution: 1.866→39.806 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.17
RfactorNum. reflection% reflection
Rfree0.2167 2372 5.12 %
Rwork0.1764 --
obs0.1784 46298 91.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.06 Å2 / Biso mean: 32.4085 Å2 / Biso min: 13.32 Å2
Refinement stepCycle: final / Resolution: 1.866→39.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 585 206 4995
Biso mean--41.68 32.56 -
Num. residues----558
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1653X-RAY DIFFRACTION0.601TORSIONAL
12B1653X-RAY DIFFRACTION0.601TORSIONAL
13C1653X-RAY DIFFRACTION0.601TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8663-1.90440.32981400.2686255691
1.9044-1.94580.24281350.2259276798
1.9458-1.99110.24611550.1924273699
1.9911-2.04090.21861660.195276699
2.0409-2.0960.3551630.284197235
2.096-2.15770.20071460.1809275699
2.1577-2.22730.20411450.1733273898
2.2273-2.30690.2081810.1997149853
2.3069-2.39930.19371570.1695276799
2.3993-2.50850.22411460.1686277798
2.5085-2.64070.22961360.1681270297
2.6407-2.80610.21071260.1826278699
2.8061-3.02270.21651590.17822822100
3.0227-3.32680.19131610.17542800100
3.3268-3.80780.23851610.17092791100
3.8078-4.79620.17671620.1484280398
4.7962-39.8060.24971330.1808288999
Refinement TLS params.Method: refined / Origin x: 11.119 Å / Origin y: -14.9474 Å / Origin z: 22.6985 Å
111213212223313233
T0.1545 Å20.001 Å2-0.0033 Å2-0.1486 Å2-0.0031 Å2--0.1427 Å2
L0.924 °20.0057 °20.1831 °2-1.1293 °20.0337 °2--1.1919 °2
S0.0048 Å °0.033 Å °0.0068 Å °-0.0498 Å °-0.0028 Å °-0.0522 Å °0.0069 Å °0.033 Å °-0.0019 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 188
2X-RAY DIFFRACTION1allB3 - 188
3X-RAY DIFFRACTION1allC3 - 188
4X-RAY DIFFRACTION1allD2 - 212
5X-RAY DIFFRACTION1allE1 - 3
6X-RAY DIFFRACTION1allF1 - 3
7X-RAY DIFFRACTION1allG301 - 303
8X-RAY DIFFRACTION1allH401 - 403

+
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