[English] 日本語
Yorodumi
- PDB-9vis: Crystal strcture of adenosylcobinamide kinase/adenosylcobinamide ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9vis
TitleCrystal strcture of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU from Akkermansia muciniphila in complex with AdoCbi-GDP
ComponentsAdenosylcobinamide kinase
KeywordsTRANSFERASE / VB12 / Cobamide remodeling / CobU / adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase / Akkermansia muciniphila
Function / homology
Function and homology information


adenosylcobinamide kinase activity / adenosylcobinamide kinase / adenosylcobinamide-phosphate guanylyltransferase / cobinamide phosphate guanylyltransferase activity / cobalamin biosynthetic process / GTP binding / ATP binding
Similarity search - Function
Cobinamide kinase/cobinamide phosphate guanyltransferase / Cobinamide kinase / cobinamide phosphate guanyltransferase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Adenosylcobinamide kinase
Similarity search - Component
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJiang, M. / Kong, C. / Wei, Q. / Guo, S. / Chen, X. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2108085MC75 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural insights into the adenosylcobinamide-phosphate guanylyltransferase activity of CobU from Akkermansia muciniphila.
Authors: Jiang, M. / Kong, C. / Wei, Q. / Guo, S. / Chen, X. / Li, Q. / Wang, M.
History
DepositionJun 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosylcobinamide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8613
Polymers22,1071
Non-polymers1,7542
Water3,567198
1
A: Adenosylcobinamide kinase
hetero molecules

A: Adenosylcobinamide kinase
hetero molecules

A: Adenosylcobinamide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5829
Polymers66,3223
Non-polymers5,2616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7050 Å2
ΔGint-40 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.729, 89.729, 89.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

-
Components

#1: Protein Adenosylcobinamide kinase / Adenosylcobinamide-phosphate guanylyltransferase


Mass: 22107.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Gene: Amuc_1678 / Production host: Escherichia coli (E. coli)
References: UniProt: B2UM52, adenosylcobinamide kinase, adenosylcobinamide-phosphate guanylyltransferase
#2: Chemical ChemComp-A1ER6 / adenosylcobinamide-GDP


Mass: 1661.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C68H93CoN21O21P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate 20% Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 20790 / % possible obs: 100 % / Redundancy: 39.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.016 / Rrim(I) all: 0.099 / Χ2: 0.991 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
1.85-1.9239.91.68720600.8340.9540.271.7080.922
1.92-1.9939.41.120460.9180.9780.1771.1140.959
1.99-2.0840.10.68320710.9710.9930.1090.6920.998
2.08-2.1939.10.50820400.980.9950.0820.5151.007
2.19-2.3339.10.32320560.9910.9980.0520.3271.085
2.33-2.5140.40.2220690.9960.9990.0350.2231.095
2.51-2.7639.10.14720570.99810.0240.1491.09
2.76-3.1639.90.09120930.99910.0150.0921.074
3.16-3.9939.30.0532109110.0090.0540.978
3.99-5037.30.0352189110.0060.0360.702

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→44.86 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 1040 5.09 %
Rwork0.1787 --
obs0.1804 20429 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 119 198 1736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051606
X-RAY DIFFRACTIONf_angle_d1.0782218
X-RAY DIFFRACTIONf_dihedral_angle_d14.671760
X-RAY DIFFRACTIONf_chiral_restr0.05231
X-RAY DIFFRACTIONf_plane_restr0.005277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.950.27051320.24732684X-RAY DIFFRACTION95
1.95-2.070.21891350.19712716X-RAY DIFFRACTION97
2.07-2.230.26191290.22282716X-RAY DIFFRACTION98
2.23-2.460.23091620.2142749X-RAY DIFFRACTION99
2.46-2.810.23491640.20742796X-RAY DIFFRACTION99
2.81-3.540.21211760.17792794X-RAY DIFFRACTION100
3.54-44.860.17861420.14332934X-RAY DIFFRACTION99

+
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