4HAP

Crystal Structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with cellobiose

• PDB DOI: https://doi.org/10.2210/pdb4HAP/pdb

• Classification: HYDROLASE
• Organism(s): Limnoria quadripunctata
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2012-09-27 Released: 2013-06-12 
• Deposition Author(s): Martin, R.N.A., McGeehan, J.E., Streeter, S.D., Cragg, S.M., Guille, M.J., Schnorr, K.M., Kern, M., Bruce, N.C., McQueen-Mason, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.144 
• R-Value Observed: 0.147 

Biological Assembly 1  

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

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

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: 94.08 kDa 
• Atom Count: 7,924 
• Modelled Residue Count: 862 
• Deposited Residue Count: 862 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH7 family protein	A, B	431	Limnoria quadripunctata	Mutation(s): 0  Gene Names: GH7B EC: 3.2.1.91
UniProt
Find proteins for D4HRL0 (Limnoria quadripunctata) Explore D4HRL0  Go to UniProtKB:  D4HRL0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CA	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	C, D	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.191 
• R-Value Work: 0.144 
• R-Value Observed: 0.147 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.26	α = 94.26
b = 54.19	β = 96.02
c = 72.45	γ = 94.99

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-12 
Deposition Author(s): Martin, R.N.A., McGeehan, J.E., Streeter, S.D., Cragg, S.M., Guille, M.J., Schnorr, K.M., Kern, M., Bruce, N.C., McQueen-Mason, S.J.

Revision History  

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary