5ZRD

Tyrosinase from Burkholderia thailandensis (BtTYR) at low pH condition

PDB DOI: https://doi.org/10.2210/pdb5ZRD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia thailandensis E264
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-24 Released: 2018-10-31
Deposition Author(s): Lee, S., Son, H.-F., Kim, K.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.221
R-Value Work: 0.180
R-Value Observed: 0.182

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural Basis for Highly Efficient Production of Catechol Derivatives at Acidic pH by Tyrosinase from Burkholderia thailandensis

Son, H.F., Lee, S.H., Lee, S.H., Kim, H., Hong, H., Lee, U.J., Lee, P.G., Kim, B.G., Kim, K.J.

(2018) ACS Catal 8: 10375-10382

DOI: https://doi.org/10.1021/acscatal.8b02635

Macromolecule Content

Total Structure Weight: 245.33 kDa
Atom Count: 17,209
Modelled Residue Count: 2,122
Deposited Residue Count: 2,196
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosinase	A, B, C, D	549	Burkholderia thailandensis E264	Mutation(s): 0 Gene Names: melO, BTH_II0649, DR63_5120 EC: 1.14.18.1
UniProt
Find proteins for Q2T7K1 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T7K1 Go to UniProtKB: Q2T7K1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2T7K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain U [auth C] SDF format, chain AA [auth D] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain M [auth B]	AA [auth D], E [auth A], M [auth B], U [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain U [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain W [auth C] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain W [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] F [auth A] BA [auth D], CA [auth D], DA [auth D], EA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], V [auth C], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain GA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	FA [auth D] GA [auth D] J [auth A] K [auth A] R [auth B] FA [auth D], GA [auth D], J [auth A], K [auth A], R [auth B], S [auth B], X [auth C], Y [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Focus chain Y [auth C]
O Query on O Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain HA [auth D] SDF format, chain L [auth A] SDF format, chain T [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B]	HA [auth D], L [auth A], T [auth B], Z [auth C]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain L [auth A] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain HA [auth D] Focus chain L [auth A] Focus chain T [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.221
R-Value Work: 0.180
R-Value Observed: 0.182
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.914	α = 90
b = 142.914	β = 90
c = 256.756	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-10-31

Deposition Author(s):

Lee, S.

Son, H.-F.

Kim, K.-J.

Revision History (Full details and data files)

Version 1.0: 2018-10-31
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary