5ZKU | pdb_00005zku

Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 in complex with DFA-III

PDB DOI: https://doi.org/10.2210/pdb5ZKU/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: 2.32 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.188 (Depositor), 0.200 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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: 285.13 kDa
Atom Count: 20,245
Modelled Residue Count: 2,653
Deposited Residue Count: 2,670
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DFA-IIIase	A, B, C, D, E A, B, C, D, E, F	445	Pseudarthrobacter chlorophenolicus A6	Mutation(s): 0 Gene Names: Achl_2895 EC: 3.2.1 (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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8HDZ1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9F3 Query on 9F3 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth E] mmCIF format, chain L [auth F]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	(2R,3'S,4'S,4aR,5'R,6R,7R,7aS)-4a,5',6-tris(hydroxymethyl)spiro[3,6,7,7a-tetrahydrofuro[2,3-b][1,4]dioxine-2,2'-oxolane ]-3',4',7-triol C₁₂ H₂₀ O₁₀ KSRQDWNGXKYIDO-TWOHWVPZSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.188 (Depositor), 0.200 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.466	α = 90
b = 77.175	β = 99.6
c = 139.718	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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Ligand Structure Quality Assessment

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 1.1: 2024-03-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 in complex with DFA-III

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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