3WQ7 | pdb_00003wq7

New crystal form of the hyperthermophilic family 12 endo-cellulase from Pyrococcus furiosus

PDB DOI: https://doi.org/10.2210/pdb3WQ7/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-01-23 Released: 2014-07-02
Deposition Author(s): Kataoka, M., Ishikawa, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.217 (Depositor), 0.216 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

A new crystal form of a hyperthermophilic endocellulase.

Kataoka, M., Ishikawa, K.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 878-883

PubMed: 25005081 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X14010930
Primary Citation Related Structures:
3WQ7

PubMed Abstract:
The hyperthermophilic glycoside hydrolase family endocellulase 12 from the archaeon Pyrococcus furiosus (EGPf; Gene ID PF0854; EC 3.2.1.4) catalyzes the hydrolytic cleavage of the β-1,4-glucosidic linkage in β-glucan in lignocellulose biomass. A crystal of EGPf was previously prepared at pH 9.0 and its structure was determined at an atomic resolution of 1.07 Å. This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal.

Organizational Affiliation

Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-hiroshima, Hiroshima 739-0046, Japan.

Macromolecule Content

Total Structure Weight: 73.66 kDa
Atom Count: 4,967
Modeled Residue Count: 540
Deposited Residue Count: 638
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase A	A, B	319	Pyrococcus furiosus	Mutation(s): 0 Gene Names: eglA EC: 3.2.1.4
UniProt
Find proteins for Q9V2T0 (Pyrococcus furiosus) Explore Q9V2T0 Go to UniProtKB: Q9V2T0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9V2T0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], U [auth B], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain U [auth B] Focus chain V [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], S [auth B], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain S [auth B] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.217 (Depositor), 0.216 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.729	α = 90
b = 62.568	β = 95.08
c = 86.284	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-02

Deposition Author(s):

Kataoka, M.

Ishikawa, K.

Revision History (Full details and data files)

Version 1.0: 2014-07-02
Type: Initial release
Version 1.1: 2014-07-16
Changes: Database references
Version 1.2: 2015-12-09
Changes: Database references
Version 1.3: 2017-11-22
Changes: Refinement description
Version 1.4: 2024-03-20
Changes: Data collection, Database references, Derived calculations

3WQ7 | pdb_00003wq7

New crystal form of the hyperthermophilic family 12 endo-cellulase from Pyrococcus furiosus

Literature

A new crystal form of a hyperthermophilic endocellulase.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand