5LHL

Crystal Structure of Two-Domain Laccase from Streptomyces griseoflavus

PDB DOI: https://doi.org/10.2210/pdb5LHL/pdb

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

Deposited: 2016-07-12 Released: 2017-08-16
Deposition Author(s): Gabdulkhakov, A.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.210
R-Value Work: 0.167
R-Value Observed: 0.169

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 griseoflavus

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

To be published.

Macromolecule Content

Total Structure Weight: 210.38 kDa
Atom Count: 13,490
Modelled Residue Count: 1,659
Deposited Residue Count: 1,932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Two-domain laccase	A, B, C, D, E A, B, C, D, E, F	322	Streptomyces griseoflavus	Mutation(s): 0 EC: 1.10.3.2
UniProt
Find proteins for A0A0M4FJ81 (Streptomyces griseoflavus) Explore A0A0M4FJ81 Go to UniProtKB: A0A0M4FJ81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0M4FJ81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth F] SDF format, chain P [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain W [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] G [auth A] GA [auth D] AA [auth D], BA [auth D], CA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth E], J [auth A], JA [auth E], KA [auth E], MA [auth E], N [auth A], O [auth A], OA [auth F], P [auth A], Q [auth B], R [auth B], S [auth B], W [auth B], X [auth C], Y [auth D], Z [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain MA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain MA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain LA [auth E] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain T [auth B]	K [auth A], LA [auth E], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain LA [auth E] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain LA [auth E] Focus chain T [auth B]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth E] SDF format, chain U [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain U [auth B] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain U [auth B]	DA [auth D] EA [auth D] L [auth A] M [auth A] NA [auth E] DA [auth D], EA [auth D], L [auth A], M [auth A], NA [auth E], U [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth E] Focus chain U [auth B] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth E] Focus chain U [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain V [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain V [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain V [auth B]	FA [auth D], V [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain V [auth B] Interactions & Density Focus chain FA [auth D] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.210
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.64	α = 90
b = 94.72	β = 90.67
c = 117.4	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

Gabdulkhakov, A.G.

Revision History (Full details and data files)

Version 1.0: 2017-08-16
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description