6Z14 | pdb_00006z14

Structure of Bifidobacterium bifidum GH20 beta-N-beta-N-acetylhexosaminidase E553Q variant in complex with 4MU-6SGlcNAc-derived oxazoline

PDB DOI: https://doi.org/10.2210/pdb6Z14/pdb

Classification: HYDROLASE
Organism(s): Bifidobacterium bifidum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-05-12 Released: 2021-05-19
Deposition Author(s): He, Y., Jin, Y., Rizkallah, P., Chen, P.
Funding Organization(s): Wellcome Trust, National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.205 (Depositor), 0.213 (DCC)
R-Value Work:
0.160 (Depositor), 0.171 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure and activity of the GH20 beta-N-beta-N-acetylhexosaminidase from Bifidobacterium bifidum

He, Y., Jin, Y.

To be published.

Macromolecule Content

Total Structure Weight: 109.16 kDa
Atom Count: 5,979
Modeled Residue Count: 694
Deposited Residue Count: 1,010
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A [auth JJJ]	1,010	Bifidobacterium bifidum	Mutation(s): 1 Gene Names: bbhII, B0085_1802, LMG11583_1629 EC: 3.2.1.52
UniProt
Find proteins for D4QAP5 (Bifidobacterium bifidum) Explore D4QAP5 Go to UniProtKB: D4QAP5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D4QAP5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q4Z (Subject of Investigation/LOI) Query on Q4Z Download:Ideal Coordinates CCD File SDF format, chain D [auth JJJ] MOL2 format, chain D [auth JJJ] mmCIF format, chain D [auth JJJ]	D [auth JJJ]	[(3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-2-methyl-6,7-bis(oxidanyl)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d][1,3]oxazol-1-ium-5-yl]methyl sulfate C₈ H₁₃ N O₈ S JTXHTZSXIURMTP-PVFLNQBWSA-N		Interactions Focus chain D [auth JJJ] Interactions & Density Focus chain D [auth JJJ]
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain C [auth JJJ] MOL2 format, chain C [auth JJJ] mmCIF format, chain C [auth JJJ]	C [auth JJJ]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain C [auth JJJ] Interactions & Density Focus chain C [auth JJJ]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain B [auth JJJ] MOL2 format, chain B [auth JJJ] mmCIF format, chain B [auth JJJ]	B [auth JJJ]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain B [auth JJJ] Interactions & Density Focus chain B [auth JJJ]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth JJJ] SDF format, chain E [auth JJJ] MOL2 format, chain F [auth JJJ] MOL2 format, chain E [auth JJJ] mmCIF format, chain F [auth JJJ] mmCIF format, chain E [auth JJJ]	E [auth JJJ], F [auth JJJ]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth JJJ] Focus chain F [auth JJJ] Interactions & Density Focus chain E [auth JJJ] Focus chain F [auth JJJ]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.205 (Depositor), 0.213 (DCC)
R-Value Work: 0.160 (Depositor), 0.171 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.423	α = 90
b = 124.884	β = 90
c = 151.682	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	209057/Z/ 17/Z
National Natural Science Foundation of China (NSFC)	China	31400663

Revision History (Full details and data files)

Version 1.0: 2021-05-19
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary