5WUT | pdb_00005wut

Crystal structure of laminarinase from Flavobacterium sp. UMI-01

PDB DOI: https://doi.org/10.2210/pdb5WUT/pdb

Classification: HYDROLASE
Organism(s): Flavobacterium sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-21 Released: 2018-01-03
Deposition Author(s): Qin, H.M., Miyakawa, Y., Nakamura, A., Tanokura, M.
Funding Organization(s): Ministry of Education, Culture, Sports, Science, and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of laminarinase from Flavobacterium sp. UMI-01

Qin, H.M., Miyakawa, Y., Nakamura, A., Tanokura, M.

To be published.

Macromolecule Content

Total Structure Weight: 54.17 kDa
Atom Count: 4,423
Modeled Residue Count: 460
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ULam111	A, B	235	Flavobacterium sp.	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.63	α = 90
b = 80.88	β = 90
c = 109.49	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-01-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science, and Technology	Japan	--

Revision History (Full details and data files)

Version 1.0: 2018-01-03
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Structure summary

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.