6G21 | pdb_00006g21

Crystal structure of an esterase from Aspergillus oryzae

PDB DOI: https://doi.org/10.2210/pdb6G21/pdb

Classification: HYDROLASE
Organism(s): Aspergillus oryzae RIB40
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2018-03-22 Released: 2018-05-23
Deposition Author(s): Moroz, O.V., Blagova, E., Davies, G.J., Wilson, K.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.194 (Depositor), 0.203 (DCC)
R-Value Work:
0.154 (Depositor), 0.165 (DCC)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of an esterase from Aspergillus oryzae

Moroz, O.V., Blagova, E., Davies, G.J., Wilson, K.S.

To be published.

Macromolecule Content

Total Structure Weight: 115.11 kDa
Atom Count: 8,444
Modeled Residue Count: 1,008
Deposited Residue Count: 1,014
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable feruloyl esterase B-2	A, B	507	Aspergillus oryzae RIB40	Mutation(s): 0 Gene Names: faeB-2, AO090001000582 EC: 3.1.1.73
UniProt
Find proteins for Q2UMX6 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore Q2UMX6 Go to UniProtKB: Q2UMX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2UMX6
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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

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] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	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] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
FER Query on FER Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth B] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B]	I [auth A], R [auth B]	3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID C₁₀ H₁₀ O₄ KSEBMYQBYZTDHS-HWKANZROSA-N		Interactions Focus chain I [auth A] Focus chain R [auth B] Interactions & Density Focus chain I [auth A] Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain S [auth B]	J [auth A], K [auth A], S [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain T [auth B] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B]	L [auth A], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain T [auth B] Interactions & Density Focus chain L [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.194 (Depositor), 0.203 (DCC)
R-Value Work: 0.154 (Depositor), 0.165 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.472	α = 90
b = 119.472	β = 90
c = 142.85	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-05-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-23
Type: Initial release
Version 1.1: 2019-04-10
Changes: Advisory, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-10-16
Changes: Data collection, Database references, Refinement description, Structure summary