8BOU | pdb_00008bou

Crystal structure of Blautia producta GH94

PDB DOI: https://doi.org/10.2210/pdb8BOU/pdb

Classification: HYDROLASE
Organism(s): Blautia producta ATCC 27340 = DSM 2950
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-15 Released: 2023-11-29
Deposition Author(s): Levy, C.W.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.222 (Depositor), 0.222 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BOU

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

Literature

Blautia producta is a competent degrader among human gut Firmicutes for utilizing dietary beta mixed linkage glucan

Singh, R.P., Thankur, R., Wagstaff, B., Kumar, G., Kurata, R., Patel, D., Miyazaki, T., Levy, C.W., Field, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 188.76 kDa
Atom Count: 13,781
Modeled Residue Count: 1,612
Deposited Residue Count: 1,648
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N,N'-diacetylchitobiose phosphorylase	A, B	824	Blautia producta ATCC 27340 = DSM 2950	Mutation(s): 0 Gene Names: E5259_00910
UniProt
Find proteins for A0A7G5MNS2 (Blautia producta) Explore A0A7G5MNS2 Go to UniProtKB: A0A7G5MNS2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7G5MNS2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES 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]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain D [auth A]	C [auth A], D [auth A], I [auth B], J [auth B], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.222 (Depositor), 0.222 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.46	α = 90
b = 135.29	β = 90
c = 166.99	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR32876/PFN/20/1471/2020

Revision History (Full details and data files)

Version 1.0: 2023-11-29
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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.