2IQ7 | pdb_00002iq7

Crystal structure of the polygalacturonase from Colletotrichum lupini and its implications for the interaction with polygalacturonase-inhibiting proteins

PDB DOI: https://doi.org/10.2210/pdb2IQ7/pdb

Classification: HYDROLASE
Organism(s): Colletotrichum lupini
Mutation(s): No

Deposited: 2006-10-13 Released: 2007-10-23
Deposition Author(s): Bonivento, D., Federici, L., Matteo, A.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.196 (Depositor), 0.200 (DCC)
R-Value Work:
0.152 (Depositor), 0.170 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins

Bonivento, D., Pontiggia, D., Matteo, A.D., Fernandez-Recio, J., Salvi, G., Tsernoglou, D., Cervone, F., Lorenzo, G.D., Federici, L.

(2008) Proteins 70: 294-299

PubMed: 17876815 Search on PubMed
DOI: https://doi.org/10.1002/prot.21610
Primary Citation of Related Structures:
2IQ7

Organizational Affiliation

Dipartimento di Scienze Biochimiche, Dipartimento di Biologia Vegetale, Università di Roma "La Sapienza," Piazzale Aldo Moro 5, 00185 Roma, Italy.

Macromolecule Content

Total Structure Weight: 244.66 kDa
Atom Count: 19,675
Modelled Residue Count: 2,372
Deposited Residue Count: 2,373
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endopolygalacturonase	A, B, C, D, E A, B, C, D, E, F, G	339	Colletotrichum lupini	Mutation(s): 0 EC: 3.2.1.15
UniProt
Find proteins for A1E266 (Colletotrichum lupini var. setosum) Explore A1E266 Go to UniProtKB: A1E266
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1E266
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	6		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G79306TC GlyCosmos: G79306TC GlyGen: G79306TC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J [auth L], K [auth M], L [auth N], M [auth O], I, J [auth L], K [auth M], L [auth N], M [auth O], N [auth Q]	2		N-Glycosylation	Interactions Focus chain I Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N] Focus chain M [auth O] Focus chain N [auth Q] Interactions & Density Focus chain I Focus chain J [auth L] Focus chain K [auth M] Focus chain L [auth N] Focus chain M [auth O] Focus chain N [auth Q]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F]	O [auth A] P [auth B] S [auth C] T [auth D] U [auth E] O [auth A], P [auth B], S [auth C], T [auth D], U [auth E], W [auth F]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain O [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth F]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain V [auth E] SDF format, chain X [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F]	Q [auth B], V [auth E], X [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain Q [auth B] Focus chain V [auth E] Focus chain X [auth F]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.196 (Depositor), 0.200 (DCC)
R-Value Work: 0.152 (Depositor), 0.170 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.64	α = 90
b = 127.266	β = 90
c = 205.828	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

Bonivento, D.

Federici, L.

Matteo, A.D.

Revision History (Full details and data files)

Version 1.0: 2007-10-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary