6GJF

Ancestral endocellulase Cel5A

PDB DOI: https://doi.org/10.2210/pdb6GJF/pdb

Classification: HYDROLASE
Organism(s): synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-05-16 Released: 2019-06-12
Deposition Author(s): Gavira, J.A., Perez-Jimenez, R., Barruetabena-Garate, N.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.153
R-Value Work: 0.118
R-Value Observed: 0.120

wwPDB Validation 3D Report Full Report

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

Literature

Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis

Barruetabena-Garate, N., Alonso-Lerma, B., Galera-Prat, A., Joudeh, N., Barandiaran, L., Aldazabal, L., Arbulu, M., Alcalde, M., De Sancho, D., Gavira, J.A., Carrion-Vazquez, M., Perez-Jimenez, R.

(2019) Commun Chem

DOI: https://doi.org/10.1038/s42004-019-0176-6

Macromolecule Content

Total Structure Weight: 203.82 kDa
Atom Count: 17,330
Modelled Residue Count: 1,818
Deposited Residue Count: 1,818
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE	A, B, C, D, E A, B, C, D, E, F	303	synthetic construct	Mutation(s): 0 EC: 3.2.1.4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain EA [auth E] SDF format, chain KA [auth E] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	CA [auth D] EA [auth E] KA [auth E] N [auth A] NA [auth F] CA [auth D], EA [auth E], KA [auth E], N [auth A], NA [auth F], O [auth A], P [auth A], T [auth B], U [auth B], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain EA [auth E] Focus chain KA [auth E] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth D] Focus chain EA [auth E] Focus chain KA [auth E] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain FA [auth E] SDF format, chain G [auth A] SDF format, chain GA [auth E] SDF format, chain H [auth A] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C]	DA [auth D] FA [auth E] G [auth A] GA [auth E] H [auth A] DA [auth D], FA [auth E], G [auth A], GA [auth E], H [auth A], HA [auth E], I [auth A], M [auth A], MA [auth F], Q [auth B], R [auth B], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain M [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain M [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain S [auth B] SDF format, chain V [auth B] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C]	AA [auth D] BA [auth D] IA [auth E] JA [auth E] K [auth A] AA [auth D], BA [auth D], IA [auth E], JA [auth E], K [auth A], L [auth A], LA [auth F], S [auth B], V [auth B], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth F] Focus chain S [auth B] Focus chain V [auth B] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth F] Focus chain S [auth B] Focus chain V [auth B] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.153
R-Value Work: 0.118
R-Value Observed: 0.120
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.436	α = 90
b = 235.636	β = 90.67
c = 74.562	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

Gavira, J.A.

Perez-Jimenez, R.

Barruetabena-Garate, N.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2016-74875-P

Revision History (Full details and data files)

Version 1.0: 2019-06-12
Type: Initial release
Version 1.1: 2019-07-10
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description