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

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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) 

Literature

Crystal structure of laminarinase from Flavobacterium sp. UMI-01

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ULam111	A, B	235	Flavobacterium sp.	Mutation(s): 0
UniProt
Find proteins for A0A1Y1CVU5 (Flavobacterium sp. UMI-01) Explore A0A1Y1CVU5  Go to UniProtKB:  A0A1Y1CVU5

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

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-03 
Deposition Author(s): Qin, H.M., Miyakawa, Y., Nakamura, A., Tanokura, M.

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

Revision History  

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