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- PDB-6ypa: The C146A variant of an amidase from Pyrococcus horikoshii with b... -

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Basic information

Entry
Database: PDB / ID: 6ypa
TitleThe C146A variant of an amidase from Pyrococcus horikoshii with bound glutaramide
ComponentsCN hydrolase domain-containing protein
KeywordsHYDROLASE / amidase of the nitrilase superfamily
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
pentanediamide / CN hydrolase domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsSewell, B.T. / Su, S. / Venter, P. / Makumire, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
CitationJournal: To Be Published
Title: The structure of the C146A variant of the amidase from Pyrococcus horikoshii bound to glutaramide suggests the basis of amide recognition.
Authors: Sewell, B.T. / Su, S. / Venter, P. / Makumire, S.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CN hydrolase domain-containing protein
B: CN hydrolase domain-containing protein
C: CN hydrolase domain-containing protein
D: CN hydrolase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5479
Polymers127,9354
Non-polymers6135
Water10,016556
1
A: CN hydrolase domain-containing protein
B: CN hydrolase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3205
Polymers63,9672
Non-polymers3523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-23 kcal/mol
Surface area18660 Å2
MethodPISA
2
C: CN hydrolase domain-containing protein
D: CN hydrolase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2284
Polymers63,9672
Non-polymers2602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-23 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.684, 100.639, 134.096
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
CN hydrolase domain-containing protein


Mass: 31983.697 Da / Num. of mol.: 4 / Mutation: C146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0642 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O58376
#2: Chemical
ChemComp-P6W / pentanediamide / Glutaramide


Mass: 130.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 2.5-4.0 mg/ml protein, 0.1 M Imidazole, MES monohydrate (acid) buffer at pH 6.5, 20% v/v Glycerol, 10% w/v PEG 4000, 0.2M Glutaramide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→100.64 Å / Num. obs: 144086 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 18.89 Å2 / Rpim(I) all: 0.042 / Rrim(I) all: 0.125 / Net I/σ(I): 8.8 / Num. measured all: 1264338
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.58-1.618.10.45757071041.0362.97199.8
4.29-100.848.646.16551676530.0150.043100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å80.49 Å
Translation2 Å80.49 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1j31

1j31


Resolution: 1.58→80.492 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.41
Details: Alternating cycles of Phenix refine and manual adjustment with coot. One cycle oof PDB-REDO
RfactorNum. reflection% reflection
Rfree0.2398 7145 4.99 %
Rwork0.2065 --
obs0.2082 143188 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97 Å2 / Biso mean: 31.1176 Å2 / Biso min: 15.31 Å2
Refinement stepCycle: final / Resolution: 1.58→80.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8497 0 42 556 9095
Biso mean--29.31 37.87 -
Num. residues----1059
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.5980.44632120.3657427994
1.598-1.61680.42052520.3641441299
1.6168-1.63650.45652070.3515447499
1.6365-1.65720.39222370.3464449299
1.6572-1.6790.37332540.3246447999
1.679-1.7020.34822160.3113445399
1.702-1.72630.3212240.3018453699
1.7263-1.75210.33572590.3029442299
1.7521-1.77950.32712600.3004447799
1.7795-1.80870.36392500.2967448299
1.8087-1.83980.32162250.267451099
1.8398-1.87330.3052440.255449099
1.8733-1.90930.30182270.2514452799
1.9093-1.94830.32152550.2416448499
1.9483-1.99070.2922140.23894560100
1.9907-2.0370.28452590.22684490100
2.037-2.08790.26962210.2251451799
2.0879-2.14440.25762430.2134536100
2.1444-2.20750.25192230.21164571100
2.2075-2.27880.26162670.21784545100
2.2788-2.36020.22722320.21214547100
2.3602-2.45470.27432290.21344578100
2.4547-2.56640.26882340.20444584100
2.5664-2.70170.25682540.20254547100
2.7017-2.8710.22162480.20714595100
2.871-3.09270.22762280.19874622100
3.0927-3.40390.24342400.19784595100
3.4039-3.89650.18022450.16954666100
3.8965-4.90910.15212160.14794717100
4.9091-80.4920.17942700.16314856100

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