6M6M | pdb_00006m6m

The crystal structure of glycosidase mutant

PDB DOI: https://doi.org/10.2210/pdb6M6M/pdb

Classification: HYDROLASE
Organism(s): Kribbella flavida DSM 17836
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2020-03-15 Released: 2021-03-17
Deposition Author(s): Wang, R.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.178 (Depositor), 0.141 (DCC)
R-Value Work:
0.134 (Depositor), 0.138 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Characterization and Structural Elucidation of Enhanced Catalytic Activity upon Engineering Glycosidase KfGH01 for the Production of Vina-ginsenoside R7

Wang, R.F.

To be published.

Macromolecule Content

Total Structure Weight: 98.96 kDa
Atom Count: 8,176
Modeled Residue Count: 893
Deposited Residue Count: 894
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A, B	447	Kribbella flavida DSM 17836	Mutation(s): 2 Gene Names: Kfla_5268 EC: 3.2.1.21
UniProt
Find proteins for D2PL27 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PL27 Go to UniProtKB: D2PL27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2PL27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS (Subject of Investigation/LOI) Query on TRS Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.178 (Depositor), 0.141 (DCC)
R-Value Work: 0.134 (Depositor), 0.138 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.734	α = 90
b = 95.432	β = 90.76
c = 93.382	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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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.