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- PDB-4pxb: The crystal structure of AtUAH in complex with (S)-ureidoglycolate -

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Basic information

Entry
Database: PDB / ID: 4pxb
TitleThe crystal structure of AtUAH in complex with (S)-ureidoglycolate
ComponentsUreidoglycolate hydrolase
KeywordsHYDROLASE / Amidase / Hydantoinase / Carbamoylase
Function / homology
Function and homology information


ureidoglycolate amidohydrolase / ureide catabolic process / ureidoglycolate hydrolase activity / allantoin catabolic process / purine nucleobase catabolic process / plastid / manganese ion binding / endoplasmic reticulum
Similarity search - Function
Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / (2S)-(carbamoylamino)(hydroxy)ethanoic acid / Ureidoglycolate hydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.903 Å
AuthorsShin, I. / Rhee, S.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural insights into the substrate specificity of (s)-ureidoglycolate amidohydrolase and its comparison with allantoate amidohydrolase.
Authors: Shin, I. / Han, K. / Rhee, S.
History
DepositionMar 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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_auth_seq_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: Ureidoglycolate hydrolase
B: Ureidoglycolate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0298
Polymers92,5422
Non-polymers4886
Water18,5731031
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-56 kcal/mol
Surface area30640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.015, 89.520, 163.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ureidoglycolate hydrolase / / AtUAH / Allantoate amidohydrolase 2 / AtAHH2 / Ureidoglycolate amidohydrolase


Mass: 46270.766 Da / Num. of mol.: 2 / Fragment: UNP residues 50-476 / Mutation: E183A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UAH, AAH2, At5g43600, K9D7.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VXY9, EC: 3.5.3.19
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UGC / (2S)-(carbamoylamino)(hydroxy)ethanoic acid / (S)-Ureidoglycolate


Mass: 134.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6N2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1031 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.45 % / Mosaicity: 0.355 ° / Mosaicity esd: 0.004 °

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 7A (6B, 6C1)10.97934
SYNCHROTRONPhoton Factory AR-NW12A20.97923, 0.97940, 0.96417
Detector
TypeIDDetectorDate
ADSC QUANTUM 270r1CCD
ADSC QUANTUM 2102CCDMar 7, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979231
30.97941
40.964171
ReflectionResolution: 1.9→50 Å / Num. obs: 80858 / % possible obs: 99.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.164 / Χ2: 1.082 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9713.70.68879301.17199.5
1.97-2.0513.70.52679701.18499.5
2.05-2.1413.70.41779721.1999.7
2.14-2.2513.80.34980211.17299.8
2.25-2.3913.80.29680201.14799.9
2.39-2.5813.90.24280571.122100
2.58-2.8414.10.18980591.07100
2.84-3.2514.20.1381371.018100
3.25-4.0914.30.08481970.903100
4.09-5013.80.07284950.87999.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.903→30.642 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 16.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1885 2000 2.48 %
Rwork0.162 --
obs0.1627 80780 99.64 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.342 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 77.7 Å2 / Biso mean: 18.785 Å2 / Biso min: 6.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.3825 Å2-0 Å2-0 Å2
2---1.2221 Å2-0 Å2
3----5.1604 Å2
Refinement stepCycle: LAST / Resolution: 1.903→30.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6396 0 22 1031 7449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076518
X-RAY DIFFRACTIONf_angle_d1.0898816
X-RAY DIFFRACTIONf_chiral_restr0.0731026
X-RAY DIFFRACTIONf_plane_restr0.0051142
X-RAY DIFFRACTIONf_dihedral_angle_d12.1432424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.903-1.95060.21611380.19425417555597
1.9506-2.00340.22261410.18965542568399
2.0034-2.06230.21331400.17955565696100
2.0623-2.12880.21021410.165355475688100
2.1288-2.20490.19971420.160655765718100
2.2049-2.29320.18171420.161255815723100
2.2932-2.39750.19341420.158156175759100
2.3975-2.52380.17611420.158756175759100
2.5238-2.68190.181430.152756205763100
2.6819-2.88880.17671440.156556345778100
2.8888-3.17920.19581440.162856695813100
3.1792-3.63870.18151430.154356935836100
3.6387-4.58190.15611470.142357475894100
4.5819-30.64610.20721510.179759646115100

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