3AKR | pdb_00003akr

Crystal structure of xylanase from Trichoderma longibrachiatum

• PDB DOI: https://doi.org/10.2210/pdb3AKR/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma longibrachiatum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-15 Released: 2011-06-01 
• Deposition Author(s): Sugahara, M., Kunishima, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Packing Space Expansion of Protein Crystallization Screening with Synthetic Zeolite as a Heteroepitaxic Nucleant

Sugahara, M., Kageyama-Morikawa, Y., Kunishima, N.

(2011) Cryst Growth Des 11: 110-120

• DOI: https://doi.org/10.1021/cg100987g

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 20.98 kDa 
• Atom Count: 1,761 
• Modeled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
xylanase	A	190	Trichoderma longibrachiatum	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for F8W669 (Trichoderma longibrachiatum) Explore F8W669  Go to UniProtKB:  F8W669

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.184 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.755	α = 90
b = 38.904	β = 110.48
c = 40.214	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Sugahara, M., Kunishima, N.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-12-25
  Changes: Derived calculations, Polymer sequence
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-10-23
  Changes: Structure summary