3PFZ | pdb_00003pfz

Crystal structure of Cel7A from Talaromyces emersonii in complex with cellotetraose

PDB DOI: https://doi.org/10.2210/pdb3PFZ/pdb

Classification: HYDROLASE
Organism(s): Rasamsonia emersonii
Expression System: Aspergillus niger
Mutation(s): No

Deposited: 2010-10-29 Released: 2011-11-02
Deposition Author(s): Qin, L., Pereira, J.H., McAndrew, R.P., Simmons, B.A., Sapra, R., Adams, P.D., Sale, K.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.143 (Depositor), 0.132 (DCC)
R-Value Work:
0.126 (Depositor), 0.115 (DCC)
R-Value Observed:
0.126 (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

Crystal structure of Cel7A from Talaromyces emersonii in complex with cellotetraose

Qin, L., Pereira, J.H., McAndrew, R.P., Simmons, B.A., Sapra, R., Adams, P.D., Sale, K.L.

To be published.

Macromolecule Content

Total Structure Weight: 49.02 kDa
Atom Count: 4,336
Modeled Residue Count: 436
Deposited Residue Count: 437
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiohydrolase 1 catalytic domain	A	437	Rasamsonia emersonii	Mutation(s): 0 Gene Names: cbh1, cbh1A EC: 3.2.1.91 (PDB Primary Data), 3.2.1 (UniProt)
UniProt
Find proteins for Q8TFL9 (Rasamsonia emersonii) Explore Q8TFL9 Go to UniProtKB: Q8TFL9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TFL9
Glycosylation
Glycosylation Sites: 2	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
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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	C	4		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G00025MO GlyCosmos: G00025MO GlyGen: G00025MO

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [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: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900011 Query on PRD_900011	C	beta-cellotetraose	Oligosaccharide / Metabolism		Interactions Focus chain C Interactions & Density Focus chain C

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005 Query on PRD_900005	D	beta-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.143 (Depositor), 0.132 (DCC)
R-Value Work: 0.126 (Depositor), 0.115 (DCC)
R-Value Observed: 0.126 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.72	α = 90
b = 74.72	β = 90
c = 169.922	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-11-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-02
Type: Initial release
Version 2.0: 2019-12-25
Changes: Derived calculations, Polymer sequence
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: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 3.2: 2024-11-20
Changes: Structure summary