3W9A | pdb_00003w9a

Crystal structure of the catalytic domain of the glycoside hydrolase family 131 protein from Coprinopsis cinerea

PDB DOI: https://doi.org/10.2210/pdb3W9A/pdb

Classification: HYDROLASE
Organism(s): Coprinopsis cinerea okayama7#130
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-04-01 Released: 2013-05-22
Deposition Author(s): Miyazaki, T., Tanaka, Y., Tamura, M., Yoshida, M., Nishikawa, A., Tonozuka, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.236 (Depositor), 0.241 (DCC)
R-Value Work:
0.188 (Depositor), 0.196 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the N-terminal domain of a glycoside hydrolase family 131 protein from Coprinopsis cinerea

Miyazaki, T., Yoshida, M., Tamura, M., Tanaka, Y., Umezawa, K., Nishikawa, A., Tonozuka, T.

(2013) FEBS Lett 587: 2193-2198

PubMed: 23711369 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2013.05.041
Primary Citation Related Structures:
3W9A

PubMed Abstract:
The crystal structure of the N-terminal putative catalytic domain of a glycoside hydrolase family 131 protein from Coprinopsis cinerea (CcGH131A) was determined. The structure of CcGH131A was found to be composed of a β-jelly roll fold and mainly consisted of two β-sheets, sheet-A and sheet-B. A concave of sheet-B, the possible active site, was wide and shallow, and three glycerol molecules were present in the concave. Arg96, Glu98, Glu138, and His218 are likely to be catalytically critical residues, and it was suggested that the catalytic mechanism of CcGH131A is different from that of typical glycosidases.

Organizational Affiliation

Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan.

Macromolecule Content

Total Structure Weight: 112.67 kDa
Atom Count: 8,434
Modeled Residue Count: 949
Deposited Residue Count: 980
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C, D	245	Coprinopsis cinerea okayama7#130	Mutation(s): 0 Gene Names: CC1G_07166
UniProt
Find proteins for A8NRB3 (Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003)) Explore A8NRB3 Go to UniProtKB: A8NRB3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8NRB3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	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 B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.236 (Depositor), 0.241 (DCC)
R-Value Work: 0.188 (Depositor), 0.196 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.2	α = 89.99
b = 68.421	β = 72.87
c = 69.168	γ = 85.81

Software Package:

Software Name	Purpose
ADSC	data collection
AutoSol	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-22
Type: Initial release
Version 1.1: 2013-06-05
Changes: Database references
Version 1.2: 2013-07-10
Changes: Database references
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary