2YZC

Crystal structure of uricase from Arthrobacter globiformis in complex with allantoate

PDB DOI: https://doi.org/10.2210/pdb2YZC/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: 1.88 Å
R-Value Free: 0.195
R-Value Work: 0.159
R-Value Observed: 0.161

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: 272.61 kDa
Atom Count: 20,334
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1AL Query on 1AL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] 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 B] 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 B] 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 B] L [auth D] M [auth E] I [auth A], J [auth B], K [auth B], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	ALLANTOATE ION C₄ H₇ N₄ O₄ NUCLJNSWZCHRKL-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] 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 B] 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: 1.88 Å
R-Value Free: 0.195
R-Value Work: 0.159
R-Value Observed: 0.161
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.498	α = 90
b = 122.942	β = 90
c = 284.784	γ = 90

Software Package:

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

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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2YZC

Crystal structure of uricase from Arthrobacter globiformis in complex with allantoate

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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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)