2YZD | pdb_00002yzd

Crystal structure of uricase from Arthrobacter globiformis in complex with 8-azaxanthin (inhibitor)

PDB DOI: https://doi.org/10.2210/pdb2YZD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Arthrobacter globiformis
Mutation(s): No

Deposited: 2007-05-05 Released: 2008-05-06
Deposition Author(s): Juan, E.C.M., Hossain, M.T., Hoque, M.M., Suzuki, K., Sekiguchi, T., Takenaka, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.239 (Depositor), 0.240 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Trapping of the uric acid substrate in the crystal structure of urate oxidase from Arthrobacter globiformis

Juan, E.C.M., Hossain, M.T., Hoque, M.M., Yamamoto, T., Imamura, S., Suzuki, K., Sekiguchi, T., Takenaka, A.

To be published.

Macromolecule Content

Total Structure Weight: 272.43 kDa
Atom Count: 19,524
Modelled Residue Count: 2,296
Deposited Residue Count: 2,416
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uricase	A, B, C, D, E A, B, C, D, E, F, G, H	302	Arthrobacter globiformis	Mutation(s): 0 EC: 1.7.3.3
UniProt
Find proteins for D0VWQ1 (Arthrobacter globiformis) Explore D0VWQ1 Go to UniProtKB: D0VWQ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWQ1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZA Query on AZA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth G] SDF format, chain P [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth G] MOL2 format, chain P [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth G] mmCIF format, chain P [auth H]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	8-AZAXANTHINE C₄ H₃ N₅ O₂ KVGVQTOQSNJTJI-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.239 (Depositor), 0.240 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.33	α = 90
b = 122.28	β = 90
c = 283.92	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-05-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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Crystal structure of uricase from Arthrobacter globiformis in complex with 8-azaxanthin (inhibitor)

Trapping of the uric acid substrate in the crystal structure of urate oxidase from Arthrobacter globiformis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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