5HO9 | pdb_00005ho9

Structure of truncated AbnA (domains 1-3), a GH43 arabinanase from Geobacilllus stearothermophilus, in complex with arabinooctaose

PDB DOI: https://doi.org/10.2210/pdb5HO9/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-01-19 Released: 2017-02-01
Deposition Author(s): Lansky, S., Salama, R., Azoulai, D., Shwartstien, O., Shoham, Y., Shoham, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.242 (Depositor), 0.243 (DCC)
R-Value Work:
0.183 (Depositor), 0.189 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of truncated AbnA (domains 1-3), a GH43 arabinanase from Geobacilllus stearothermophilus, in complex with arabinooctaose

Lansky, S., Salama, R., Shwartstien, O., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 147.81 kDa
Atom Count: 9,874
Modeled Residue Count: 1,192
Deposited Residue Count: 1,278
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular arabinanase	A, B	639	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: abnA
UniProt
Find proteins for B3EYN2 (Geobacillus stearothermophilus) Explore B3EYN2 Go to UniProtKB: B3EYN2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3EYN2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose	C, D	8		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G91389JD GlyCosmos: G91389JD

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B]	CA [auth B] DA [auth B] EA [auth B] FA [auth B] GA [auth B] CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] E [auth A] F [auth A] G [auth A] AA [auth B], BA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.242 (Depositor), 0.243 (DCC)
R-Value Work: 0.183 (Depositor), 0.189 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.172	α = 90
b = 129.172	β = 90
c = 488.364	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-02-01
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: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary