4N8U | pdb_00004n8u

Two-Domain Laccase from Streptomyces viridochromogenes at 2.4 A resolution AC629

PDB DOI: https://doi.org/10.2210/pdb4N8U/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces viridochromogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-18 Released: 2014-10-29
Deposition Author(s): Gabdulkhakov, A., Tischenko, S., Yurevich, L., Lisov, A., Leontievsky, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.188 (Depositor), 0.200 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Two-Domain Laccase from Streptomyces viridochromogenes at 2.4 A resolution AC629

Gabdulkhakov, A., Tischenko, S., Yurevich, L., Lisov, A., Leontievsky, A.

To be published.

Macromolecule Content

Total Structure Weight: 92.85 kDa
Atom Count: 6,478
Modeled Residue Count: 826
Deposited Residue Count: 843
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multicopper oxidase	A, B, C	281	Streptomyces viridochromogenes	Mutation(s): 0 EC: 1.10.3.2
UniProt
Find proteins for J9S5G3 (Streptomyces viridochromogenes) Explore J9S5G3 Go to UniProtKB: J9S5G3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J9S5G3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], O [auth C], P [auth C], Q [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain R [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C]	G [auth A] H [auth A] M [auth B] N [auth B] R [auth C] G [auth A], H [auth A], M [auth B], N [auth B], R [auth C], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.188 (Depositor), 0.200 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.72	α = 90
b = 79.6	β = 90
c = 204.05	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-10-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-29
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description