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
UniProt
Find proteins for A0ACD6B9D9 (Flavobacterium sp. UMI-01) Explore A0ACD6B9D9 Go to UniProtKB: A0ACD6B9D9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0ACD6B9D9
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.