4XEB | pdb_00004xeb

The structure of P. funicolosum Cel7A

PDB DOI: https://doi.org/10.2210/pdb4XEB/pdb

Classification: HYDROLASE
Organism(s): Talaromyces funiculosus
Expression System: Trichoderma reesei QM6a
Mutation(s): No

Deposited: 2014-12-23 Released: 2016-06-22
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.203 (Depositor), 0.195 (DCC)
R-Value Work:
0.138 (Depositor)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

Engineering enhanced cellobiohydrolase activity

Taylor, L.E., Knott, B.C., Baker, J.O., Alahuhta, P.M., Hobdey, S.E., Linger, J.G., Lunin, V.V., Amore, A., Subramanian, V., Podkaminer, K., Xu, Q., VanderWall, T.A., Schuster, L.A., Chaudhari, Y.B., Adney, W.S., Crowley, M.F., Himmel, M.E., Decker, S.R., Beckham, G.T.

(2018) Nat Commun 9(1): 1186

Macromolecule Content

Total Structure Weight: 48.02 kDa
Atom Count: 4,316
Modeled Residue Count: 430
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A	436	Talaromyces funiculosus	Mutation(s): 0 Gene Names: cbh1 EC: 3.2.1
UniProt
Find proteins for F1CYZ0 (Talaromyces funiculosus) Explore F1CYZ0 Go to UniProtKB: F1CYZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1CYZ0
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	6		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G09454VW GlyCosmos: G09454VW GlyGen: G09454VW

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

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

Biologically Interesting Molecules (External Reference)

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005 Query on PRD_900005	B	beta-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain B Interactions & Density Focus chain B

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900020 Query on PRD_900020	C	beta-cellohexaose	Oligosaccharide / Metabolism		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203 (Depositor), 0.195 (DCC)
R-Value Work: 0.138 (Depositor)
R-Value Observed: 0.140 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.972	α = 90
b = 61.836	β = 98.77
c = 85.849	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-22

Deposition Author(s):

Alahuhta, P.M.

Lunin, V.V.

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC36-08GO28308

Revision History (Full details and data files)

Version 1.0: 2016-06-22
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2017-11-22
Changes: Refinement description
Version 1.3: 2018-05-30
Changes: Data collection, Database references
Version 2.0: 2019-12-04
Changes: Author supporting evidence, Polymer sequence
Version 2.1: 2019-12-25
Changes: Database references
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 3.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.2: 2024-10-16
Changes: Structure summary