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- PDB-8wv2: Crystal structure of urethanase from Candida parapsilosis and str... -

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Basic information

Entry
Database: PDB / ID: 8wv2
TitleCrystal structure of urethanase from Candida parapsilosis and structure-based Engineering to improve the catalytic activity and stability
ComponentsAmidase family protein
KeywordsHYDROLASE / urethanase
Function / homologyAmidase signature domain / Amidase signature (AS) superfamily / Amidase / hydrolase activity / Amidase domain-containing protein
Function and homology information
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsZhao, T. / Wu, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of urethanase from Candida parapsilosis and structure-based Engineering to improve the catalytic activity and stability
Authors: Zhao, T.
History
DepositionOct 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidase family protein
B: Amidase family protein
C: Amidase family protein
E: Amidase family protein
F: Amidase family protein
G: Amidase family protein
H: Amidase family protein
D: Amidase family protein


Theoretical massNumber of molelcules
Total (without water)494,4588
Polymers494,4588
Non-polymers00
Water17,240957
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.420, 110.158, 180.584
Angle α, β, γ (deg.)75.84, 83.62, 73.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Amidase family protein


Mass: 61807.234 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: FOB60_005225 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A679EIJ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 957 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 12% w/v PEG 8000, 0.1 M Tris-HCl, and pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.66→49.56 Å / Num. obs: 128604 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.88 Å2 / CC1/2: 0.925 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.158 / Rrim(I) all: 0.289 / Net I/σ(I): 7.9 / Num. measured all: 439740 / Scaling rejects: 11525
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.66-2.710.8092162563380.5870.5190.9662.697.8
14.57-49.560.06426147730.9880.0410.07616.696.5

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→48.91 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 6315 4.92 %
Rwork0.2044 --
obs0.206 128461 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34832 0 0 957 35789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00535680
X-RAY DIFFRACTIONf_angle_d0.82848488
X-RAY DIFFRACTIONf_dihedral_angle_d16.25213200
X-RAY DIFFRACTIONf_chiral_restr0.0515368
X-RAY DIFFRACTIONf_plane_restr0.0066240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.69020.31622220.28384004X-RAY DIFFRACTION98
2.6902-2.72190.29792200.27494035X-RAY DIFFRACTION98
2.7219-2.75510.31011800.27034205X-RAY DIFFRACTION98
2.7551-2.78990.32961910.28624002X-RAY DIFFRACTION98
2.7899-2.82660.34972180.29944069X-RAY DIFFRACTION98
2.8266-2.86540.31781950.27884062X-RAY DIFFRACTION98
2.8654-2.90630.29252120.26614076X-RAY DIFFRACTION98
2.9063-2.94970.27292200.26224032X-RAY DIFFRACTION98
2.9497-2.99580.30612260.25994070X-RAY DIFFRACTION98
2.9958-3.04490.30122350.25634043X-RAY DIFFRACTION98
3.0449-3.09740.29672250.26044007X-RAY DIFFRACTION98
3.0974-3.15370.28322340.24734135X-RAY DIFFRACTION98
3.1537-3.21430.28812060.24454032X-RAY DIFFRACTION99
3.2143-3.27990.252080.23724070X-RAY DIFFRACTION99
3.2799-3.35120.26992100.24814160X-RAY DIFFRACTION99
3.3512-3.42910.29642100.24764009X-RAY DIFFRACTION99
3.4291-3.51490.25292200.21964099X-RAY DIFFRACTION98
3.5149-3.60990.27172170.21334004X-RAY DIFFRACTION98
3.6099-3.71610.23942130.20264113X-RAY DIFFRACTION99
3.7161-3.8360.22822150.18734057X-RAY DIFFRACTION99
3.836-3.9730.21012010.1794131X-RAY DIFFRACTION99
3.973-4.1320.20811810.17044084X-RAY DIFFRACTION99
4.132-4.320.20112020.16624120X-RAY DIFFRACTION99
4.32-4.54760.18632280.15624089X-RAY DIFFRACTION98
4.5476-4.83230.15721870.14614070X-RAY DIFFRACTION98
4.8323-5.2050.17172390.14384008X-RAY DIFFRACTION98
5.205-5.7280.18891870.16214097X-RAY DIFFRACTION98
5.728-6.55520.19272020.16634098X-RAY DIFFRACTION99
6.5552-8.25240.15522180.14444068X-RAY DIFFRACTION98
8.2524-48.910.18561930.15174097X-RAY DIFFRACTION98

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