7DSZ | pdb_00007dsz

Crystal structure of Amuc_1102 from Akkermansia muciniphila

PDB DOI: https://doi.org/10.2210/pdb7DSZ/pdb

Classification: MOTOR PROTEIN
Organism(s): Akkermansia muciniphila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-04 Released: 2021-02-24
Deposition Author(s): Xiang, R., Wang, J., Wang, Y., Zhang, M., Wang, M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.200 (Depositor), 0.201 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Amuc_1102 fromAkkermansia muciniphilaadopts animmunoglobulin-like fold related to archaeal type IV pilus

Xiang, R., Wang, J., Xu, W., Zhang, M., Wang, M.

(2021) Biochem Biophys Res Commun 547: 59-64

DOI: https://doi.org/10.1016/j.bbrc.2021.02.022

Macromolecule Content

Total Structure Weight: 80.34 kDa
Atom Count: 5,399
Modeled Residue Count: 568
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amuc_1102	A, B, C	232	Akkermansia muciniphila	Mutation(s): 0 Gene Names: Amuc_1102
UniProt
Find proteins for B2UR43 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc)) Explore B2UR43 Go to UniProtKB: B2UR43
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2UR43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth B], G [auth C], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.200 (Depositor), 0.201 (DCC)
R-Value Work: 0.172 (Depositor), 0.173 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.469	α = 90
b = 83.941	β = 90
c = 107.252	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SHELXDE	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	KJ2019ZD02

Revision History (Full details and data files)

Version 1.0: 2021-02-24
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.