5ZL4 | pdb_00005zl4

Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 wihout its lid in complex with GF2

PDB DOI: https://doi.org/10.2210/pdb5ZL4/pdb

Classification: HYDROLASE
Organism(s): Pseudarthrobacter chlorophenolicus A6
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-03-26 Released: 2018-12-19
Deposition Author(s): Yu, S.H., Shen, H., Li, X., Mu, W.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.179 (Depositor), 0.200 (DCC)
R-Value Work:
0.147 (Depositor), 0.166 (DCC)
R-Value Observed:
0.149 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZL4

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

Literature

Structural and functional basis of difructose anhydride III hydrolase, which sequentially converts inulin using the same catalytic residue

Yu, S.H., Shen, H., Cheng, Y.Y., Zhu, Y.Y., Li, X., Mu, W.M.

(2018) ACS Catal 8: 10683-10697

DOI: https://doi.org/10.1021/acscatal.8b02424

Macromolecule Content

Total Structure Weight: 45.33 kDa
Atom Count: 3,191
Modeled Residue Count: 416
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DFA-IIIase	A	420	Pseudarthrobacter chlorophenolicus A6	Mutation(s): 0 Gene Names: Achl_2895 EC: 4.2.2.18 (PDB Primary Data), 4.2.2.17 (UniProt)
UniProt
Find proteins for B8HDZ1 (Pseudarthrobacter chlorophenolicus (strain ATCC 700700 / DSM 12829 / CIP 107037 / JCM 12360 / KCTC 9906 / NCIMB 13794 / A6)) Explore B8HDZ1 Go to UniProtKB: B8HDZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8HDZ1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G11260CN GlyCosmos: G11260CN

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900029 Query on PRD_900029	B	1-kestose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.179 (Depositor), 0.200 (DCC)
R-Value Work: 0.147 (Depositor), 0.166 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.407	α = 90
b = 187.407	β = 90
c = 187.407	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-12-19
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-03-27
Changes: Data collection, Database references, 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.