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- PDB-1uf5: Crystal structure of C171A/V236A Mutant of N-carbamyl-D-amino aci... -

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Basic information

Entry
Database: PDB / ID: 1uf5
TitleCrystal structure of C171A/V236A Mutant of N-carbamyl-D-amino acid amidohydrolase complexed with N-carbamyl-D-methionine
ComponentsN-carbamyl-D-amino acid amidohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


N-carbamoyl-D-amino-acid hydrolase / N-carbamoyl-D-amino acid hydrolase activity
Similarity search - Function
: / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-METHYLSULFANYL-2-UREIDO-BUTYRIC ACID / N-carbamoyl-D-amino acid hydrolase
Similarity search - Component
Biological speciesAgrobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHashimoto, H. / Aoki, M. / Shimizu, T. / Nakai, T. / Morikawa, H. / Ikenaka, Y. / Takahashi, S. / Sato, M.
CitationJournal: To be published
Title: Crystal structure of C171A/V236A mutant of N-carbamyl-D-amino acid amidohydrolase
Authors: Hashimoto, H. / Aoki, M. / Shimizu, T. / Nakai, T. / Morikawa, H. / Ikenaka, Y. / Takahashi, S. / Sato, M.
History
DepositionMay 23, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-carbamyl-D-amino acid amidohydrolase
B: N-carbamyl-D-amino acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7245
Polymers68,2782
Non-polymers4473
Water13,763764
1
A: N-carbamyl-D-amino acid amidohydrolase
B: N-carbamyl-D-amino acid amidohydrolase
hetero molecules

A: N-carbamyl-D-amino acid amidohydrolase
B: N-carbamyl-D-amino acid amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,44910
Polymers136,5564
Non-polymers8936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)67.424, 137.275, 67.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein N-carbamyl-D-amino acid amidohydrolase


Mass: 34138.977 Da / Num. of mol.: 2 / Mutation: C171A/V236A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium sp. (bacteria) / Plasmid: pAD108 / Production host: Escherichia coli (E. coli)
References: UniProt: P60327, N-carbamoyl-D-amino-acid hydrolase
#2: Chemical ChemComp-CDT / 4-METHYLSULFANYL-2-UREIDO-BUTYRIC ACID / N-CARBAMYL-D-METHIONINE


Mass: 192.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.21 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→39.27 Å / Num. obs: 81286

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.27 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.198 -
Rwork0.178 -
obs-81286
Refinement stepCycle: LAST / Resolution: 1.6→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 28 764 5600

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