5C1E

Crystal Structure of the Pectin Methylesterase from Aspergillus niger in Penultimately Deglycosylated Form (N-acetylglucosamine Stub at Asn84)

PDB DOI: https://doi.org/10.2210/pdb5C1E/pdb

Classification: HYDROLASE
Organism(s): Aspergillus niger ATCC 1015
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2015-06-13 Released: 2015-07-01
Deposition Author(s): Jameson, G.B., Williams, M.A.K., Loo, T.S., Kent, L.M., Melton, L.D., Mercadante, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.202
R-Value Work: 0.171
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 33.05 kDa
Atom Count: 2,746
Modelled Residue Count: 299
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectinesterase	A	299	Aspergillus niger ATCC 1015	Mutation(s): 0 Gene Names: ASPNIDRAFT_214857 EC: 3.1.1.11
UniProt
Find proteins for G3YAL0 (Aspergillus niger (strain ATCC 1015 / CBS 113.46 / FGSC A1144 / LSHB Ac4 / NCTC 3858a / NRRL 328 / USDA 3528.7)) Explore G3YAL0 Go to UniProtKB: G3YAL0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G3YAL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A]	I [auth A], J [auth A], K [auth A], L [auth A], N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.202
R-Value Work: 0.171
R-Value Observed: 0.172
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.614	α = 90
b = 113.543	β = 90
c = 88.765	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
MrBUMP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-07-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-01
Type: Initial release
Version 1.1: 2015-12-02
Changes: Database references
Version 1.2: 2016-02-03
Changes: Database references
Version 1.3: 2017-11-01
Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary

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5C1E

Crystal Structure of the Pectin Methylesterase from Aspergillus niger in Penultimately Deglycosylated Form (N-acetylglucosamine Stub at Asn84)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)