9XCC | pdb_00009xcc

Apg mutant enzyme D336A of acarbose hydrolase from human gut flora K. grimontii TD1, complex with maltotriose

PDB DOI: https://doi.org/10.2210/pdb9XCC/pdb

Classification: HYDROLASE
Organism(s): Klebsiella grimontii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-10-25 Released: 2026-10-28
Deposition Author(s): Zhou, J.H., Huang, J.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.262 (Depositor), 0.261 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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Literature

Apg mutant enzyme D336A of acarbose hydrolase from human gut flora K. grimontii TD1, complex with maltotriose

Zhou, J.H., Huang, J.Y.

To be published.

Macromolecule Content

Total Structure Weight: 69.57 kDa
Atom Count: 4,898
Modeled Residue Count: 599
Deposited Residue Count: 605
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin glucosidase	A	605	Klebsiella grimontii	Mutation(s): 1 Gene Names: tvaI, malZ, HV064_03130, NCTC9149_05459 EC: 3.2.1.135 (PDB Primary Data), 3.2.1.20 (PDB Primary Data)
UniProt
Find proteins for A0A7H4P971 (Klebsiella grimontii) Explore A0A7H4P971 Go to UniProtKB: A0A7H4P971
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7H4P971
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.262 (Depositor), 0.261 (DCC)
R-Value Work: 0.212 (Depositor), 0.213 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.554	α = 90
b = 75.554	β = 90
c = 400.589	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release