6SUD

Structure of L320A mutant of Rex8A from Paenibacillus barcinonensis complexed with xylose.

PDB DOI: https://doi.org/10.2210/pdb6SUD/pdb

Classification: HYDROLASE
Organism(s): Paenibacillus barcinonensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-09-13 Released: 2020-05-27
Deposition Author(s): Jimenez-Ortega, E., Ramirez-Escudero, M., Sanz-Aparicio, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.277
R-Value Work: 0.242
R-Value Observed: 0.244

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 90.53 kDa
Atom Count: 6,953
Modelled Residue Count: 754
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reducing-end xylose-releasing exo-oligoxylanase Rex8A	A, B	382	Paenibacillus barcinonensis	Mutation(s): 1 Gene Names: rex8A, DFQ00_11062 EC: 3.2.1.156
UniProt
Find proteins for A0A0S2UQQ5 (Paenibacillus barcinonensis) Explore A0A0S2UQQ5 Go to UniProtKB: A0A0S2UQQ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0S2UQQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYP (Subject of Investigation/LOI) Query on XYP Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain U [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B]	J [auth A], K [auth A], U [auth B]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain U [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain N [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	D [auth A], N [auth B], R [auth B], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain N [auth B] Focus chain R [auth B] Focus chain S [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [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 I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth B] MOL2 format, chain C [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 I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth B]	C [auth A] E [auth A] F [auth A] G [auth A] H [auth A] C [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], O [auth B], P [auth B], Q [auth B], T [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] 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 L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] 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 L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.277
R-Value Work: 0.242
R-Value Observed: 0.244
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.514	α = 87.83
b = 59.172	β = 78.35
c = 79.412	γ = 74.61

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-27

Deposition Author(s):

Jimenez-Ortega, E.

Ramirez-Escudero, M.

Sanz-Aparicio, J.

Revision History (Full details and data files)

Version 1.0: 2020-05-27
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2020-12-30
Changes: Database references, Structure summary
Version 2.2: 2024-01-24
Changes: Data collection, Database references, Refinement description