4YGU | pdb_00004ygu

Crystal structure of a putative adhesin (BACEGG_01763) from Bacteroides eggerthii DSM 20697 at 2.20 A resolution

PDB DOI: https://doi.org/10.2210/pdb4YGU/pdb

Classification: CELL ADHESION
Organism(s): Bacteroides eggerthii DSM 20697
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-02-26 Released: 2015-03-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.240 (Depositor), 0.260 (DCC)
R-Value Work:
0.209 (Depositor), 0.230 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a putative adhesin (BACEGG_01763) from Bacteroides eggerthii DSM 20697 at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 80.97 kDa
Atom Count: 5,263
Modeled Residue Count: 677
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative adhesin	A, B, C, D	184	Bacteroides eggerthii DSM 20697	Mutation(s): 0 Gene Names: BACEGG_01763
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] MOL2 format, chain U [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] mmCIF format, chain U [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C]	M [auth C], N [auth C], U [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain N [auth C] Focus chain U [auth D] Interactions & Density Focus chain M [auth C] Focus chain N [auth C] Focus chain U [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D], X [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240 (Depositor), 0.260 (DCC)
R-Value Work: 0.209 (Depositor), 0.230 (DCC)
R-Value Observed: 0.210 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34599

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.318	α = 90
b = 101.555	β = 90
c = 137.313	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHARP	phasing
XDS	data scaling
BUSTER	refinement
XSCALE	data scaling
SHELXD	phasing
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-03-11

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2015-03-11
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description, Source and taxonomy
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references
Version 1.4: 2024-11-20
Changes: Data collection, Structure summary