Macromolecule Content

Total Structure Weight: 44.45 kDa
Atom Count: 3409
Modelled Residue Count: 371
Deposited Residue Count: 405
Unique protein chains: 1

5Z3D

Glycosidase F290Y

DOI: 10.2210/pdb5Z3D/pdb

Classification: HYDROLASE
Organism(s): Kribbella flavida DSM 17836
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-01-05 Released: 2019-05-15
Deposition Author(s): Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.
Funding Organization(s): Platform for Drug Discovery, Informatics, and Structural Life Science(PDIS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.134
R-Value Work: 0.113
R-Value Observed: 0.114

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Glycosidase F290Y

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

To be published.

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase 15-related protein	A	405	Kribbella flavida DSM 17836	Mutation(s): 1 Gene Names: Kfla_1896 EC: 3.2.1.205
UniProt
Find proteins for D2PPM8 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PPM8 Go to UniProtKB: D2PPM8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.134
R-Value Work: 0.113
R-Value Observed: 0.114
Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.725	α = 90
b = 104.725	β = 90
c = 89.319	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2018-01-05
Released Date: 2019-05-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Platform for Drug Discovery, Informatics, and Structural Life Science(PDIS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.