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- PDB-6oha: Yeast Guanine Deaminase -

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Basic information

Entry
Database: PDB / ID: 6oha
TitleYeast Guanine Deaminase
ComponentsProbable guanine deaminase
KeywordsHYDROLASE / amidohydrolase guanine deaminase purine metabolism
Function / homology
Function and homology information


Purine catabolism / guanine deaminase / guanine deaminase activity / guanine catabolic process / guanine metabolic process / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Guanine deaminase / : / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
XANTHINE / Probable guanine deaminase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsShek, R.S. / French, J.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124898 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103403 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structural Determinants for Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily.
Authors: Shek, R. / Hilaire, T. / Sim, J. / French, J.B.
History
DepositionApr 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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: Probable guanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4909
Polymers55,2691
Non-polymers1,2218
Water4,954275
1
A: Probable guanine deaminase
hetero molecules

A: Probable guanine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,98018
Polymers110,5392
Non-polymers2,44116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area8510 Å2
ΔGint-170 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.812, 106.812, 114.178
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-508-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable guanine deaminase / Guanine aminase / Guanine aminohydrolase / GAH


Mass: 55269.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GUD1, YDL238C / Production host: Escherichia coli (E. coli) / References: UniProt: Q07729, guanine deaminase

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Non-polymers , 5 types, 283 molecules

#2: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 17% Peg 3350 0.2 M ammonium sulfate 100 mM Hepes, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.21→29.07 Å / Num. obs: 33428 / % possible obs: 99.1 % / Redundancy: 8.8 % / Biso Wilson estimate: 32.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Net I/σ(I): 10
Reflection shellResolution: 2.21→2.29 Å / Rmerge(I) obs: 0.973 / Num. unique obs: 3075 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OOD

2ood


Resolution: 2.21→29.07 Å / SU ML: 0.2169 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2395
RfactorNum. reflection% reflection
Rfree0.2034 1748 5.23 %
Rwork0.1559 --
obs0.1584 33417 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.42 Å2
Refinement stepCycle: LAST / Resolution: 2.21→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 70 275 3855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01183679
X-RAY DIFFRACTIONf_angle_d1.13934997
X-RAY DIFFRACTIONf_chiral_restr0.0574574
X-RAY DIFFRACTIONf_plane_restr0.0082633
X-RAY DIFFRACTIONf_dihedral_angle_d6.69192979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.270.27431380.22332367X-RAY DIFFRACTION91.09
2.27-2.350.23541350.18862620X-RAY DIFFRACTION99.93
2.35-2.430.27981580.17742601X-RAY DIFFRACTION99.17
2.43-2.530.18681340.15752628X-RAY DIFFRACTION99.93
2.53-2.640.23171280.15292633X-RAY DIFFRACTION99.96
2.64-2.780.20711380.15042655X-RAY DIFFRACTION99.96
2.78-2.960.20971540.1572622X-RAY DIFFRACTION99.96
2.96-3.190.21691710.15852635X-RAY DIFFRACTION100
3.19-3.510.18911320.15822668X-RAY DIFFRACTION100
3.51-4.010.17991620.1372674X-RAY DIFFRACTION100
4.01-5.050.17751630.12542682X-RAY DIFFRACTION99.13
5.05-29.070.20631350.1782884X-RAY DIFFRACTION99.67

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