6JE0 | pdb_00006je0

Ligand complex structure of GH10 family xylanase XynAF1, soaking for 30 minutes

PDB DOI: https://doi.org/10.2210/pdb6JE0/pdb

Classification: HYDROLASE
Organism(s): Aspergillus fumigatus Z5
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2019-02-02 Released: 2020-05-20
Deposition Author(s): Li, G., Miao, Y., Zhang, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.170 (Depositor), 0.171 (DCC)
R-Value Work:
0.139 (Depositor), 0.140 (DCC)
R-Value Observed:
0.141 (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 GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5

Li, G., Miao, Y., Zhang, R.

To be published.

Macromolecule Content

Total Structure Weight: 70.97 kDa
Atom Count: 5,749
Modeled Residue Count: 638
Deposited Residue Count: 638
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	319	Aspergillus fumigatus Z5	Mutation(s): 0 Gene Names: Y699_04481 EC: 3.2.1.8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	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
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C, D, E, F	2		N/A	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G87728WL GlyCosmos: G87728WL

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 G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B]	J [auth A], K [auth A], N [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	H [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116 Query on PRD_900116	C, D, E, F	4beta-beta-xylobiose	Oligosaccharide / Metabolism		Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.170 (Depositor), 0.171 (DCC)
R-Value Work: 0.139 (Depositor), 0.140 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.426	α = 73.97
b = 57.357	β = 80.8
c = 64.91	γ = 68.77

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-20

Deposition Author(s):

Li, G.

Miao, Y.

Zhang, R.

Revision History (Full details and data files)

Version 1.0: 2020-05-20
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

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Ligand complex structure of GH10 family xylanase XynAF1, soaking for 30 minutes

Crystal structure of GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5

Entity ID: 1

Entity Groups

Glycosylation

Sequence Annotations

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Entity ID: 2

Glycosylation Resources