3WRG | pdb_00003wrg

The complex structure of HypBA1 with L-arabinose

PDB DOI: https://doi.org/10.2210/pdb3WRG/pdb

Classification: HYDROLASE
Organism(s): Bifidobacterium longum subsp. longum JCM 1217
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-02-25 Released: 2014-09-03
Deposition Author(s): Huang, C.H., Zhu, Z., Cheng, Y.S., Chan, H.C., Ko, T.P., Chen, C.C., Wang, I., Ho, M.R., Hsu, S.T., Zeng, Y.F., Huang, Y.N., Liu, J.R., Guo, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.244 (Depositor), 0.243 (DCC)
R-Value Work:
0.204 (Depositor), 0.201 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure and Catalytic Mechanism of a Glycoside Hydrolase Family-127 beta-L-Arabinofuranosidase (HypBA1)

Huang, C.H., Zhu, Z., Cheng, Y.S., Chan, H.C., Ko, T.P., Chen, C.C., Wang, I., Ho, M.R., Hsu, S.T., Zeng, Y.F., Huang, Y.N., Liu, J.R., Guo, R.T.

(2014) J Bioprocess Biotech 4: 1000171-1000171

DOI: https://doi.org/10.4172/2155-9821.1000171

Macromolecule Content

Total Structure Weight: 73.39 kDa
Atom Count: 5,471
Modeled Residue Count: 658
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-reducing end beta-L-arabinofuranosidase	A	658	Bifidobacterium longum subsp. longum JCM 1217	Mutation(s): 0 Gene Names: hypBA1 EC: 3.2.1.185
UniProt
Find proteins for E8MGH8 (Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b)) Explore E8MGH8 Go to UniProtKB: E8MGH8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E8MGH8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUB Query on FUB Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	beta-L-arabinofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-KLVWXMOXSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.244 (Depositor), 0.243 (DCC)
R-Value Work: 0.204 (Depositor), 0.201 (DCC)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.586	α = 90
b = 77.586	β = 90
c = 254.176	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-03
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2024-03-20
Changes: Data collection, Database references, Structure summary