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- PDB-1uf4: Crystal structure of C171A/V236A Mutant of N-carbamyl-D-amino aci... -

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Basic information

Entry
Database: PDB / ID: 1uf4
TitleCrystal structure of C171A/V236A Mutant of N-carbamyl-D-amino acid amidohydrolase
ComponentsN-carbamyl-D-amino acid amidohydrolase
KeywordsHYDROLASE / N-carbamyl-D-amino acid amidohydrolase / D-amino acid
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 domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-carbamoyl-D-amino acid hydrolase
Similarity search - Component
Biological speciesAgrobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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
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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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


Theoretical massNumber of molelcules
Total (without water)68,2782
Polymers68,2782
Non-polymers00
Water7,638424
1
A: N-carbamyl-D-amino acid amidohydrolase
B: N-carbamyl-D-amino acid amidohydrolase

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


Theoretical massNumber of molelcules
Total (without water)136,5564
Polymers136,5564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)67.264, 136.848, 67.762
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.13 Å3/Da / Density % sol: 41.77 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→68.43 Å / Num. obs: 34273 / Biso Wilson estimate: 22.7 Å2

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→68.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1873417.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3413 10 %RANDOM
Rwork0.201 ---
obs0.201 34215 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.3958 Å2 / ksol: 0.361501 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.73 Å20 Å20 Å2
2---9.44 Å20 Å2
3---1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.15→68.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 0 424 5232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 542 9.7 %
Rwork0.274 5053 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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