8F9L | pdb_00008f9l

Intramolecular ester bond-containing repeat domain from Gemella massiliensis adhesin

PDB DOI: https://doi.org/10.2210/pdb8F9L/pdb

Classification: CELL ADHESION
Organism(s): Gemella massiliensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-23 Released: 2024-06-19
Deposition Author(s): Jin, S., Young, P.G., Squire, C.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.265 (Depositor), 0.270 (DCC)
R-Value Work:
0.231 (Depositor), 0.240 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Intramolecular ester bond-containing repeat domain from Gemella massiliensis adhesin

Jin, S., Young, P.G., Squire, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 33.77 kDa
Atom Count: 2,187
Modeled Residue Count: 281
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adhesin	A, B	152	Gemella massiliensis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.265 (Depositor), 0.270 (DCC)
R-Value Work: 0.231 (Depositor), 0.240 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.164	α = 90
b = 63.037	β = 90
c = 96.488	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

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.