5UVE | pdb_00005uve

Crystal Structure of the ABC Transporter Substrate-binding protein BAB1_0226 from Brucella abortus

PDB DOI: https://doi.org/10.2210/pdb5UVE/pdb

Classification: HYDROLASE
Organism(s): Brucella abortus 2308
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-20 Released: 2017-03-08
Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Hero, J., Babnigg, G., Crosson, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.277 (Depositor), 0.278 (DCC)
R-Value Work:
0.226 (Depositor), 0.227 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of Beta-barrel-like Protein of Unknown Function

Kim, Y., Bigelow, L., Endres, M., Babnigg, G., Crosson, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 240.02 kDa
Atom Count: 16,923
Modeled Residue Count: 2,247
Deposited Residue Count: 2,256
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Substrate-binding region of ABC-type glycine betaine transport system	A, B, C, D, E A, B, C, D, E, F, G, H	282	Brucella abortus 2308	Mutation(s): 0 Gene Names: BAB1_0226
UniProt
Find proteins for Q2YP76 (Brucella abortus (strain 2308)) Explore Q2YP76 Go to UniProtKB: Q2YP76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YP76
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain J [auth B] MOL2 format, chain O [auth E] MOL2 format, chain J [auth B] mmCIF format, chain O [auth E] mmCIF format, chain J [auth B]	J [auth B], O [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain O [auth E] Interactions & Density Focus chain J [auth B] Focus chain O [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain N [auth E] SDF format, chain P [auth F] SDF format, chain R [auth H] SDF format, chain Q [auth G] SDF format, chain M [auth D] SDF format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain M [auth D] MOL2 format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain M [auth D] mmCIF format, chain K [auth B]	I [auth A] K [auth B] L [auth C] M [auth D] N [auth E] I [auth A], K [auth B], L [auth C], M [auth D], N [auth E], P [auth F], Q [auth G], R [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.277 (Depositor), 0.278 (DCC)
R-Value Work: 0.226 (Depositor), 0.227 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.602	α = 95.19
b = 92.738	β = 110.87
c = 95.124	γ = 111.35

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-03-08

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-03-08
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2019-12-04
Changes: Author supporting evidence
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-11-20
Changes: Structure summary

5UVE | pdb_00005uve

Crystal Structure of the ABC Transporter Substrate-binding protein BAB1_0226 from Brucella abortus

Literature

Crystal Structure of Beta-barrel-like Protein of Unknown Function

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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