6GJF | pdb_00006gjf

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 (Depositor), 0.154 (DCC)
R-Value Work:
0.118 (Depositor), 0.120 (DCC)
R-Value Observed:
0.120 (Depositor)

Starting Model: experimental
View more details

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
Modeled Residue Count: 1,818
Deposited Residue Count: 1,818
Unique protein chains: 1

Macromolecules

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| 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

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] mmCIF 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] mmCIF format, chain CA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth C] mmCIF 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] mmCIF format, chain DA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF 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] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain V [auth B] mmCIF 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 (Depositor), 0.154 (DCC)
R-Value Work: 0.118 (Depositor), 0.120 (DCC)
R-Value Observed: 0.120 (Depositor)

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

View more in-depth experimental data

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