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- PDB-4e2q: Crystal Structure of (S)-Ureidoglycine Aminohydrolase from Arabid... -

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Basic information

Entry
Database: PDB / ID: 4e2q
TitleCrystal Structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana
ComponentsUreidoglycine aminohydrolase
KeywordsHYDROLASE / Bi-Cupin / Aminohydrolase / Manganese Binding / Endoplasmic Reticulum
Function / homology
Function and homology information


(S)-ureidoglycine aminohydrolase / ureidoglycine aminohydrolase activity / ureide catabolic process / allantoin catabolic process / purine nucleobase catabolic process / DNA-binding transcription factor activity / regulation of DNA-templated transcription / endoplasmic reticulum / metal ion binding / cytosol
Similarity search - Function
(S)-ureidoglycine aminohydrolase, C-terminal cupin domain / (S)-ureidoglycine aminohydrolase, N-terminal cupin domain / (S)-ureidoglycine aminohydrolase / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / (S)-ureidoglycine aminohydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsShin, I. / Rhee, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana
Authors: Shin, I. / Percudani, R. / Rhee, S.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Ureidoglycine aminohydrolase
B: Ureidoglycine aminohydrolase
C: Ureidoglycine aminohydrolase
D: Ureidoglycine aminohydrolase
E: Ureidoglycine aminohydrolase
F: Ureidoglycine aminohydrolase
G: Ureidoglycine aminohydrolase
H: Ureidoglycine aminohydrolase
I: Ureidoglycine aminohydrolase
J: Ureidoglycine aminohydrolase
K: Ureidoglycine aminohydrolase
L: Ureidoglycine aminohydrolase
M: Ureidoglycine aminohydrolase
N: Ureidoglycine aminohydrolase
O: Ureidoglycine aminohydrolase
P: Ureidoglycine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)484,54932
Polymers483,67016
Non-polymers87916
Water13,187732
1
A: Ureidoglycine aminohydrolase
B: Ureidoglycine aminohydrolase
C: Ureidoglycine aminohydrolase
D: Ureidoglycine aminohydrolase
G: Ureidoglycine aminohydrolase
I: Ureidoglycine aminohydrolase
J: Ureidoglycine aminohydrolase
K: Ureidoglycine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,27416
Polymers241,8358
Non-polymers4408
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27540 Å2
ΔGint-260 kcal/mol
Surface area71050 Å2
MethodPISA
2
E: Ureidoglycine aminohydrolase
F: Ureidoglycine aminohydrolase
H: Ureidoglycine aminohydrolase
L: Ureidoglycine aminohydrolase
M: Ureidoglycine aminohydrolase
N: Ureidoglycine aminohydrolase
O: Ureidoglycine aminohydrolase
P: Ureidoglycine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,27416
Polymers241,8358
Non-polymers4408
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27610 Å2
ΔGint-259 kcal/mol
Surface area70940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.856, 175.773, 155.176
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ureidoglycine aminohydrolase / (S)-Ureidoglycine Aminohydrolase / UGlyAH


Mass: 30229.371 Da / Num. of mol.: 16 / Fragment: UNP residues 36-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ylbA, UGLYAH, At4g17050, AT4G17050 / Plasmid: pET28a_TEV / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3)
References: UniProt: Q8GXV5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 7% (w/v) PEG 8000, 8% (w/v) ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97973 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2010
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97973 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 152515 / Num. obs: 137345 / Observed criterion σ(F): 2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.6 / % possible all: 94.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXAUTOMRmodel building
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAUTOMRphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.286 15170 -RANDOM
Rwork0.224 ---
all-152515 --
obs-137345 89.1 %-
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.888 Å20 Å2-2.5 Å2
2---4.44 Å20 Å2
3----2.448 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33216 0 16 732 33964
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00911
X-RAY DIFFRACTIONc_angle_d1.49
X-RAY DIFFRACTIONc_mcbond_it1.0391.5
X-RAY DIFFRACTIONc_scbond_it1.4912
X-RAY DIFFRACTIONc_mcangle_it1.7052
X-RAY DIFFRACTIONc_scangle_it2.1482.5
LS refinement shellResolution: 2.5→2.59 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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