4LGN | pdb_00004lgn

The structure of Acidothermus cellulolyticus family 74 glycoside hydrolase

PDB DOI: https://doi.org/10.2210/pdb4LGN/pdb

Classification: CELLULOSE BINDING PROTEIN
Organism(s): Acidothermus cellulolyticus 11B
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-28 Released: 2013-12-11
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.196 (Depositor), 0.205 (DCC)
R-Value Work:
0.150 (Depositor), 0.161 (DCC)
R-Value Observed:
0.152 (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

Structure of Acidothermus cellulolyticus family 74 glycoside hydrolase at 1.82 angstrom resolution.

Alahuhta, M., Adney, W.S., Himmel, M.E., Lunin, V.V.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1335-1338

PubMed: 24316824 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309113030005
Primary Citation Related Structures:
4LGN

PubMed Abstract:
Here, a 1.82 Å resolution X-ray structure of a glycoside hydrolase family 74 (GH74) enzyme from Acidothermus cellulolyticus is reported. The resulting structure was refined to an R factor of 0.150 and an Rfree of 0.196. Structural analysis shows that five related structures have been reported with a secondary-structure similarity of between 75 and 89%. The five similar structures were all either Clostridium thermocellum or Geotrichum sp. M128 GH74 xyloglucanases. Structural analysis indicates that the A. cellulolyticus GH74 enzyme is an endoxyloglucanase, as it lacks a characteristic loop that blocks one end of the active site in exoxyloglucanases. Superimposition with the C. thermocellum GH74 shows that Asp451 and Asp38 are the catalytic residues.

Organizational Affiliation

BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA.

Macromolecule Content

Total Structure Weight: 81.46 kDa
Atom Count: 6,908
Modeled Residue Count: 739
Deposited Residue Count: 749
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulose-binding, family II	A	749	Acidothermus cellulolyticus 11B	Mutation(s): 0 Gene Names: Acel_0618
UniProt
Find proteins for A0LSI1 (Acidothermus cellulolyticus (strain ATCC 43068 / DSM 8971 / 11B)) Explore A0LSI1 Go to UniProtKB: A0LSI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0LSI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A]	U [auth A], V [auth A], W [auth A], X [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] 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 T [auth A] MOL2 format, chain S [auth A] 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 T [auth A] mmCIF format, chain S [auth A] 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], S [auth A], T [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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 S [auth A] Focus chain T [auth A] 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 S [auth A] Focus chain T [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain AA [auth A]	AA [auth A], Y [auth A], Z [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain KA [auth A] SDF format, chain JA [auth A] SDF format, chain IA [auth A] SDF format, chain HA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain HA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain HA [auth A]	HA [auth A], IA [auth A], JA [auth A], KA [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Interactions & Density Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain FA [auth A] SDF format, chain EA [auth A] SDF format, chain DA [auth A] SDF format, chain CA [auth A] SDF format, chain BA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain BA [auth A]	BA [auth A] CA [auth A] DA [auth A] EA [auth A] FA [auth A] BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Interactions & Density Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.196 (Depositor), 0.205 (DCC)
R-Value Work: 0.150 (Depositor), 0.161 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.761	α = 90
b = 78.686	β = 90
c = 143.952	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-12-11

Deposition Author(s):

Alahuhta, P.M.

Lunin, V.V.

Revision History (Full details and data files)

Version 1.0: 2013-12-11
Type: Initial release
Version 1.1: 2014-01-15
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description