3PL3 | pdb_00003pl3

Crystal structure of Cel7A from Talaromyces emersonii in complex with cellopentaose

PDB DOI: https://doi.org/10.2210/pdb3PL3/pdb

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

Deposited: 2010-11-12 Released: 2011-12-14
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: 1.18 Å
R-Value Free:
0.150 (Depositor), 0.144 (DCC)
R-Value Work:
0.127 (Depositor), 0.121 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 4.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 49.29 kDa
Atom Count: 4,329
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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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	D	5		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G91683DU GlyCosmos: G91683DU

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	E	3		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G14338VK GlyCosmos: G14338VK GlyGen: G14338VK

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [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: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900016 Query on PRD_900016	D	beta-cellopentaose	Oligosaccharide / Metabolism		Interactions Focus chain D Interactions & Density Focus chain D

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900021 Query on PRD_900021	E	beta-cellotriose	Oligosaccharide / Metabolism		Interactions Focus chain E Interactions & Density Focus chain E

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.18 Å
R-Value Free: 0.150 (Depositor), 0.144 (DCC)
R-Value Work: 0.127 (Depositor), 0.121 (DCC)
R-Value Observed: 0.127 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.204	α = 90
b = 74.204	β = 90
c = 175.457	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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Entry History

Deposition Data

Released Date: 2011-12-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-12-14
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: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 4.0: 2020-10-14
Changes: Atomic model, Structure summary
Version 4.1: 2023-09-06
Changes: Data collection, Database references, Refinement description