4XNN | pdb_00004xnn

Crystal Structure of a GH7 Family Cellobiohydrolase from Daphnia pulex

PDB DOI: https://doi.org/10.2210/pdb4XNN/pdb

Classification: HYDROLASE
Organism(s): Daphnia pulex
Expression System: Trichoderma reesei QM6a
Mutation(s): No

Deposited: 2015-01-15 Released: 2016-01-27
Deposition Author(s): Ebrahim, A., Hobdey, S.E., Podkaminer, K., Taylor II, L.E., Beckham, G.T., Decker, S.R., Himmel, M.E., Cragg, S.M., McGeehan, J.E.
Funding Organization(s): Biotechnology and Biological Sciences Research Council, Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.209 (Depositor), 0.215 (DCC)
R-Value Work:
0.164 (Depositor), 0.173 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 3.3 of the entry. See complete history.

Literature

Characterization of a GH7 Family Cellobiohydrolase from Daphnia pulex

Hobdey, S.E., Ebrahim, A., Podkaminer, K., Taylor II, L.E., Beckham, G.T., Decker, S.R., Himmel, M.E., Cragg, S.M., McGeehan, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 96.64 kDa
Atom Count: 7,307
Modeled Residue Count: 890
Deposited Residue Count: 890
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiohydrolase CHBI	A, B	445	Daphnia pulex	Mutation(s): 0 Gene Names: CEL7A, DAPPUDRAFT_347598 EC: 3.2.1.91
UniProt
Find proteins for E9G5J5 (Daphnia pulex) Explore E9G5J5 Go to UniProtKB: E9G5J5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E9G5J5
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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A, B	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.209 (Depositor), 0.215 (DCC)
R-Value Work: 0.164 (Depositor), 0.173 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.29	α = 90
b = 47.02	β = 108.23
c = 173.5	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/L001926/1
Department of Energy (DOE, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-01-27
Type: Initial release
Version 2.0: 2017-08-30
Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
Version 3.0: 2020-03-11
Changes: Polymer sequence
Version 3.1: 2022-03-30
Changes: Author supporting evidence, Data collection, Database references, Refinement description, Source and taxonomy
Version 3.2: 2024-01-10
Changes: Data collection, Refinement description
Version 3.3: 2024-11-20
Changes: Structure summary