4ZH5 | pdb_00004zh5

Crystal structure of Endoglucanase from Perinereis brevicirris with Cellobiose

• PDB DOI: https://doi.org/10.2210/pdb4ZH5/pdb

• Classification: HYDROLASE
• Organism(s): Perinereis brevicirris
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2015-04-24 Released: 2016-06-29 
• Deposition Author(s): Fewings, R.S., Swiderska, A., Sanchez-Weatherby, J., Sorensen, T.-M., Schnorr, K.M., Kneale, G.G., McGeehan, J.E.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.115 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Starting Model: experimental

Literature

Biophysical and structural characterisation of the endoglucanase from Perinereis brevicirris

Fewings, R.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.55 kDa 
• Atom Count: 7,961 
• Modeled Residue Count: 850 
• Deposited Residue Count: 852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A, B	426	Perinereis brevicirris	Mutation(s): 0  Gene Names: pnbEG EC: 3.2.1.4
UniProt
Find proteins for F2Z7L1 (Perinereis brevicirris) Explore F2Z7L1  Go to UniProtKB:  F2Z7L1

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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 1.35 Å
• R-Value Free:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.115 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.15	α = 90
b = 108.17	β = 90
c = 112.68	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Fewings, R.S., Swiderska, A., Sanchez-Weatherby, J., Sorensen, T.-M., Schnorr, K.M., Kneale, G.G., McGeehan, J.E.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	LBNet_BIV02_Jan15McGeehan

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 2.0: 2017-08-30
  Changes: Atomic model, Author supporting evidence, Derived calculations
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 3.2: 2024-11-13
  Changes: Structure summary