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- PDB-8i99: N-carbamoyl-D-amino-acid hydrolase mutant - M4Th3 -

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Basic information

Entry
Database: PDB / ID: 8i99
TitleN-carbamoyl-D-amino-acid hydrolase mutant - M4Th3
ComponentsN-carbamoyl-D-amino-acid hydrolase
KeywordsHYDROLASE / carbon-nitrogen hydrolase / tetramer
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
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 speciesNitratireductor indicus C115 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsHu, J.M. / Ni, Y. / Xu, G.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077054 China
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Engineering the Thermostability of a d-Carbamoylase Based on Ancestral Sequence Reconstruction for the Efficient Synthesis of d-Tryptophan.
Authors: Hu, J. / Chen, X. / Zhang, L. / Zhou, J. / Xu, G. / Ni, Y.
History
DepositionFeb 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-carbamoyl-D-amino-acid hydrolase
B: N-carbamoyl-D-amino-acid hydrolase
C: N-carbamoyl-D-amino-acid hydrolase
D: N-carbamoyl-D-amino-acid hydrolase


Theoretical massNumber of molelcules
Total (without water)138,3494
Polymers138,3494
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-76 kcal/mol
Surface area40300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.143, 73.548, 77.711
Angle α, β, γ (deg.)84.08, 88.20, 89.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
N-carbamoyl-D-amino-acid hydrolase


Mass: 34587.133 Da / Num. of mol.: 4 / Mutation: S202P, E208D, R277L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratireductor indicus C115 (bacteria)
Gene: NA8A_19058 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K2NMS4

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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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris pH6.5, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 22, 2022 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.17→23.98 Å / Num. obs: 26181 / % possible obs: 98.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 4
Reflection shellResolution: 3.17→3.39 Å / Rmerge(I) obs: 0.307 / Num. unique obs: 4578

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Processing

Software
NameVersionClassification
PHENIXv1.20refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→23.98 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 1334 5.1 %
Rwork0.2008 --
obs0.2047 26172 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.17→23.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9680 0 0 0 9680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.291
X-RAY DIFFRACTIONf_dihedral_angle_d7.5651370
X-RAY DIFFRACTIONf_chiral_restr0.0671410
X-RAY DIFFRACTIONf_plane_restr0.0151768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.290.32221140.27552263X-RAY DIFFRACTION90
3.29-3.420.37211240.24862524X-RAY DIFFRACTION100
3.42-3.570.29761390.222514X-RAY DIFFRACTION100
3.57-3.760.27631750.20642466X-RAY DIFFRACTION100
3.76-3.990.30121500.19252472X-RAY DIFFRACTION100
3.99-4.30.26071250.18862539X-RAY DIFFRACTION100
4.3-4.730.223950.17112546X-RAY DIFFRACTION100
4.73-5.410.2187690.17482581X-RAY DIFFRACTION100
5.41-6.790.2881300.20722510X-RAY DIFFRACTION100
6.79-23.980.23892130.17672423X-RAY DIFFRACTION99

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