5ZN6 | pdb_00005zn6

Crystal structure of GH31 alpha-xylosidase from a soil metagenome

PDB DOI: https://doi.org/10.2210/pdb5ZN6/pdb

Classification: HYDROLASE
Organism(s): soil metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-07 Released: 2019-04-10
Deposition Author(s): Matsuzawa, T., Nakamichi, Y., Watanabe, M., Yaoi, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.195 (Depositor), 0.178 (DCC)
R-Value Work:
0.174 (Depositor)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZN6

This is version 1.1 of the entry. See complete history.

Literature

Structural insight into substrate specificity of alpha-xylosidase from a soil metagenome

Matsuzawa, T., Nakamichi, Y., Watanabe, M., Yaoi, K.

To be published.

Macromolecule Content

Total Structure Weight: 631.78 kDa
Atom Count: 47,599
Modeled Residue Count: 5,421
Deposited Residue Count: 5,496
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-xylosidase MeXyl31	A B C D E A, B, C, D, E, F, G [auth H], H [auth G]	687	soil metagenome	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BA [auth C] SDF format, chain BB [auth H] SDF format, chain CA [auth C] SDF format, chain CB [auth G] SDF format, chain DA [auth C] SDF format, chain DB [auth G] SDF format, chain EB [auth G] SDF format, chain FA [auth C] SDF format, chain FB [auth G] SDF format, chain GA [auth C] SDF format, chain GB [auth G] SDF format, chain HA [auth D] SDF format, chain HB [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain UA [auth H] SDF format, chain V [auth B] SDF format, chain VA [auth H] SDF format, chain W [auth B] SDF format, chain WA [auth H] SDF format, chain X [auth B] SDF format, chain XA [auth H] SDF format, chain Y [auth B] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] SDF format, chain Z [auth C] SDF format, chain EA [auth C] SDF format, chain AA [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth G] MOL2 format, chain EB [auth G] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth H] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth H] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain AB [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth H] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth G] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth G] mmCIF format, chain EB [auth G] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth G] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth G] mmCIF format, chain HA [auth D] mmCIF format, chain HB [auth G] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth H] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth H] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth H] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth H] mmCIF format, chain ZA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] AB [auth H] BA [auth C] BB [auth H] CA [auth C] AA [auth C], AB [auth H], BA [auth C], BB [auth H], CA [auth C], CB [auth G], DA [auth C], DB [auth G], EA [auth C], EB [auth G], FA [auth C], FB [auth G], GA [auth C], GB [auth G], HA [auth D], HB [auth G], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth E], O [auth A], OA [auth E], P [auth A], PA [auth E], Q [auth A], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth H], V [auth B], VA [auth H], W [auth B], WA [auth H], X [auth B], XA [auth H], Y [auth B], YA [auth H], Z [auth C], ZA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth H] Focus chain V [auth B] Focus chain VA [auth H] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth B] Focus chain XA [auth H] Focus chain Y [auth B] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth H] Focus chain V [auth B] Focus chain VA [auth H] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth B] Focus chain XA [auth H] Focus chain Y [auth B] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.195 (Depositor), 0.178 (DCC)
R-Value Work: 0.174 (Depositor)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.146	α = 90
b = 124.174	β = 116.81
c = 177.453	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.