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- PDB-2q37: Crystal structure of OHCU decarboxylase in the presence of (S)-al... -

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Basic information

Entry
Database: PDB / ID: 2q37
TitleCrystal structure of OHCU decarboxylase in the presence of (S)-allantoin
ComponentsOHCU decarboxylase
KeywordsPLANT PROTEIN / LYASE / OHCU / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline
Function / homology
Function and homology information


regulation of cell growth by extracellular stimulus / allantoin biosynthetic process / regulation of brassinosteroid mediated signaling pathway / regulation of seedling development / hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / response to brassinosteroid / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / brassinosteroid mediated signaling pathway ...regulation of cell growth by extracellular stimulus / allantoin biosynthetic process / regulation of brassinosteroid mediated signaling pathway / regulation of seedling development / hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / response to brassinosteroid / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / brassinosteroid mediated signaling pathway / cold acclimation / urate catabolic process / extrinsic component of cytoplasmic side of plasma membrane / purine nucleobase metabolic process / protein tetramerization / cytoplasmic side of plasma membrane / peroxisome / identical protein binding / cytosol
Similarity search - Function
Bifunctional hydroxyisourate hydrolase/2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / UraD-like / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Hydroxyisourate hydrolase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase superfamily / OHCU decarboxylase / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site ...Bifunctional hydroxyisourate hydrolase/2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / UraD-like / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Hydroxyisourate hydrolase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase superfamily / OHCU decarboxylase / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-[(4S)-2,5-DIOXOIMIDAZOLIDIN-4-YL]UREA / Uric acid degradation bifunctional protein TTL
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKim, K.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and functional basis for (s)-allantoin formation in the ureide pathway.
Authors: Kim, K. / Park, J. / Rhee, S.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OHCU decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9952
Polymers20,8371
Non-polymers1581
Water37821
1
A: OHCU decarboxylase
hetero molecules

A: OHCU decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9914
Polymers41,6742
Non-polymers3162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)73.582, 73.582, 69.647
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by crystallographic symmetric operation.

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Components

#1: Protein OHCU decarboxylase / Transthyretin-like protein


Mass: 20837.164 Da / Num. of mol.: 1 / Fragment: residues 1-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TTL / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LVM5
#2: Chemical ChemComp-3AL / 1-[(4S)-2,5-DIOXOIMIDAZOLIDIN-4-YL]UREA / (S)-ALLANTOIN


Mass: 158.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5), 20 mM MgCl2, 16% polyacrylic acid 5100, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97948, 0.97961, 0.97181, 0.97956
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 19, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELMADMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979481
20.979611
30.971811
40.979561
ReflectionResolution: 2.5→50 Å / Num. all: 7845 / Num. obs: 7843 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.095
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.479 / Num. unique all: 7845 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 748 -RANDOM
Rwork0.215 ---
all0.215 7843 --
obs0.215 7528 96 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1127 0 11 21 1159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.461
X-RAY DIFFRACTIONc_scbond_it2.47
X-RAY DIFFRACTIONc_mcangle_it2.527
X-RAY DIFFRACTIONc_scangle_it3.543

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