4JGL | pdb_00004jgl

Crystal structure of a streptavidin-like protein (BACEGG_01519) from Bacteroides eggerthii DSM 20697 at 1.25 A resolution

PDB DOI: https://doi.org/10.2210/pdb4JGL/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Bacteroides eggerthii DSM 20697
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-03-01 Released: 2013-04-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.153 (Depositor), 0.160 (DCC)
R-Value Work:
0.134 (Depositor), 0.140 (DCC)
R-Value Observed:
0.135 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a hypothetical protein (BACEGG_01519) from Bacteroides eggerthii DSM 20697 at 1.25 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 19.16 kDa
Atom Count: 1,534
Modeled Residue Count: 152
Deposited Residue Count: 169
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A	169	Bacteroides eggerthii DSM 20697	Mutation(s): 0 Gene Names: BACEGG_01519, ZP_03458740.1
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
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
UNL Query on UNL Download Ideal Coordinates CCD File	B [auth A]	Unknown ligand BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.153 (Depositor), 0.160 (DCC)
R-Value Work: 0.134 (Depositor), 0.140 (DCC)
R-Value Observed: 0.135 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34JGL

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.322	α = 90
b = 79.322	β = 90
c = 50.113	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 1.1: 2014-12-24
Changes: Structure summary
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-06
Changes: Data collection, 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.