6YZD

Crystal structure of the M295A variant of Ssl1

PDB DOI: https://doi.org/10.2210/pdb6YZD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces sviceus ATCC 29083
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-05-06 Released: 2021-05-12
Deposition Author(s): Mielenbrink, S., Olbrich, A., Urlacher, V., Span, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.225
R-Value Work: 0.200

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Effect of the axial ligand mutation on spectral and structural properties of Ssl1 laccase

Mielenbrink, S., Olbrich, A., Urlacher, V., Span, I.

To be published.

Macromolecule Content

Total Structure Weight: 107.76 kDa
Atom Count: 6,573
Modelled Residue Count: 811
Deposited Residue Count: 975
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper oxidase	A [auth AAA], B [auth BBB], C [auth CCC]	325	Streptomyces sviceus ATCC 29083	Mutation(s): 1 Gene Names: SSEG_02446
UniProt
Find proteins for B5HSR1 (Streptomyces sviceus (strain ATCC 29083 / DSM 924 / JCM 4929 / NBRC 13980 / NCIMB 11184 / NRRL 5439 / UC 5370)) Explore B5HSR1 Go to UniProtKB: B5HSR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5HSR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth AAA] SDF format, chain S [auth CCC] MOL2 format, chain I [auth AAA] MOL2 format, chain S [auth CCC] mmCIF format, chain I [auth AAA] mmCIF format, chain S [auth CCC]	I [auth AAA], S [auth CCC]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth AAA] Focus chain S [auth CCC] Interactions & Density Focus chain I [auth AAA] Focus chain S [auth CCC]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain J [auth BBB] SDF format, chain K [auth BBB] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] SDF format, chain O [auth CCC] SDF format, chain P [auth CCC] SDF format, chain Q [auth CCC] SDF format, chain R [auth CCC] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain J [auth BBB] MOL2 format, chain K [auth BBB] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain O [auth CCC] MOL2 format, chain P [auth CCC] MOL2 format, chain Q [auth CCC] MOL2 format, chain R [auth CCC] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain J [auth BBB] mmCIF format, chain K [auth BBB] mmCIF format, chain L [auth BBB] mmCIF format, chain M [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain O [auth CCC] mmCIF format, chain P [auth CCC] mmCIF format, chain Q [auth CCC] mmCIF format, chain R [auth CCC]	D [auth AAA] E [auth AAA] F [auth AAA] G [auth AAA] H [auth AAA] D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], J [auth BBB], K [auth BBB], L [auth BBB], M [auth BBB], N [auth BBB], O [auth CCC], P [auth CCC], Q [auth CCC], R [auth CCC]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain O [auth CCC] Focus chain P [auth CCC] Focus chain Q [auth CCC] Focus chain R [auth CCC] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain O [auth CCC] Focus chain P [auth CCC] Focus chain Q [auth CCC] Focus chain R [auth CCC]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.225
R-Value Work: 0.200
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.44	α = 90
b = 104.1	β = 90
c = 163.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description