6JHX | pdb_00006jhx

Crystal structure of alginate-binding protein AlgQ2 without calcium ion

• PDB DOI: https://doi.org/10.2210/pdb6JHX/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Sphingomonas sp.
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-02-19 Released: 2020-02-19 
• Deposition Author(s): Okumura, K., Maruyama, Y., Murata, K., Hashimoto, W.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of alginate-binding protein AlgQ2 without calcium ion

Okumura, K., Maruyama, Y., Mikami, B., Murata, K., Hashimoto, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 115.41 kDa 
• Atom Count: 8,246 
• Modeled Residue Count: 969 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AlgQ2	A, B	492	Sphingomonas sp.	Mutation(s): 2  Gene Names: algQ2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid	C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G72509DQ GlyCosmos:  G72509DQ

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.873	α = 80.37
b = 60.824	β = 89.81
c = 87.228	γ = 88.17

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Okumura, K., Maruyama, Y., Murata, K., Hashimoto, W.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	--

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary