4ZG8 | pdb_00004zg8

Crystal structure of Endoglucanase from Perinereis brevicirris

PDB DOI: https://doi.org/10.2210/pdb4ZG8/pdb

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

Deposited: 2015-04-22 Released: 2016-06-29
Deposition Author(s): Fewings, R.S., Swiderska, A., Sanchez-Weatherby, J., Sorensen, T.L.-M., Schnorr, K.M., Kneale, G.G., McGeehan, J.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.148 (Depositor), 0.148 (DCC)
R-Value Work:
0.110 (Depositor), 0.109 (DCC)
R-Value Observed:
0.112 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Biophysical and structural characterisation of the endoglucanase from Perinereis brevicirris

Fewings, R.S.

To be published.

Macromolecule Content

Total Structure Weight: 94.51 kDa
Atom Count: 7,905
Modeled Residue Count: 851
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2Z7L1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B], N [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] H [auth A] I [auth B] D [auth A], E [auth A], F [auth A], H [auth A], I [auth B], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.148 (Depositor), 0.148 (DCC)
R-Value Work: 0.110 (Depositor), 0.109 (DCC)
R-Value Observed: 0.112 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.6	α = 90
b = 110.34	β = 90
c = 113.02	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Fewings, R.S.

Swiderska, A.

Sanchez-Weatherby, J.

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary