5LXZ | pdb_00005lxz

W288A mutant of GlxA from Streptomyces lividans: Cu-bound form

PDB DOI: https://doi.org/10.2210/pdb5LXZ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptomyces lividans TK24
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-09-23 Released: 2017-07-26
Deposition Author(s): Chaplin, A.K., Hough, M.A., Worrall, J.A.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.181 (Depositor), 0.180 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The role of a second-coordination sphere tryptophan residue in the maturation of the catalytic metalloradical site in the auxillary activity family 5 (AA5) GlxA from Streptomyces lividans

Chaplin, A.K., Svistunenko, D.A., Hough, M.A., Wilson, M.T., Vijgenboom, E., Worrall, J.A.R.

To be published.

Macromolecule Content

Total Structure Weight: 67.1 kDa
Atom Count: 5,547
Modeled Residue Count: 601
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secreted protein	A [auth B]	604	Streptomyces lividans TK24	Mutation(s): 1 Gene Names: SLIV_23470

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	F [auth B], G [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain F [auth B] Focus chain G [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain B SDF format, chain C [auth B] MOL2 format, chain B MOL2 format, chain C [auth B] mmCIF format, chain B mmCIF format, chain C [auth B]	B, C [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B Focus chain C [auth B] Interactions & Density Focus chain B Focus chain C [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] 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 H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] 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 H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] 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]	H [auth B] I [auth B] J [auth B] K [auth B] L [auth B] H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] 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 H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] 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]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	D [auth B], E [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.181 (Depositor), 0.180 (DCC)
R-Value Work: 0.163 (Depositor), 0.163 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.51	α = 90
b = 80.87	β = 90
c = 140.29	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-07-26

Deposition Author(s):

Chaplin, A.K.

Hough, M.A.

Worrall, J.A.R.

Revision History (Full details and data files)

Version 1.0: 2017-07-26
Type: Initial release
Version 1.1: 2024-01-17
Changes: Advisory, Data collection, Database references, Refinement description