4NAJ | pdb_00004naj

Crystal Structure of Two-Domain Laccase from Streptomyces Lividans AC1709 in complex with azide after 90 min soaking

PDB DOI: https://doi.org/10.2210/pdb4NAJ/pdb

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

Deposited: 2013-10-22 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: 2.60 Å
R-Value Free:
0.208 (Depositor), 0.212 (DCC)
R-Value Work:
0.169 (Depositor), 0.175 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Two-Domain Laccase from Streptomyces Lividans AC1709 in complex with azide after 90 min soaking

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

To be published.

Macromolecule Content

Total Structure Weight: 39.06 kDa
Atom Count: 2,406
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 EC: 1.10.3.2

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE5 Query on PE5 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C₁₈ H₃₈ O₉ CUDPPTPIUWYGFI-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
7PE Query on 7PE Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL C₁₄ H₃₀ O₇ UKXKPKBTMYNOFS-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [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]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	F [auth A], M [auth A], N [auth A]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain F [auth A] Focus chain M [auth A] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.208 (Depositor), 0.212 (DCC)
R-Value Work: 0.169 (Depositor), 0.175 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.02	α = 90
b = 177.02	β = 90
c = 177.02	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

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: Advisory, Refinement description
Version 1.2: 2023-11-08
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary