4GYB | pdb_00004gyb

Two-domain laccase from streptomyces lividans at 2.4 A resolution AC1709

PDB DOI: https://doi.org/10.2210/pdb4GYB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces lividans TK24
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-05 Released: 2013-10-02
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:
0.177 (Depositor), 0.181 (DCC)
R-Value Work:
0.154 (Depositor), 0.157 (DCC)
R-Value Observed:
0.155 (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

Two-domain laccase from streptomyces lividans at 2.4 A resolution AC1709

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

To be published.

Macromolecule Content

Total Structure Weight: 37.93 kDa
Atom Count: 2,394
Modeled Residue Count: 279
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper oxidase	A	343	Streptomyces lividans TK24	Mutation(s): 0 Gene Names: SSPG_00990

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	H [auth A], K [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain K [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.177 (Depositor), 0.181 (DCC)
R-Value Work: 0.154 (Depositor), 0.157 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.54	α = 90
b = 177.54	β = 90
c = 177.54	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-10-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-02
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description