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- PDB-6oh9: Yeast Guanine Deaminase -

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Basic information

Entry
Database: PDB / ID: 6oh9
TitleYeast Guanine Deaminase
ComponentsYeast 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
Probable guanine deaminase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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: Yeast Guanine Deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,37710
Polymers55,2691
Non-polymers2,1089
Water7,855436
1
A: Yeast Guanine Deaminase
hetero molecules

A: Yeast Guanine Deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,75420
Polymers110,5392
Non-polymers4,21518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area8450 Å2
ΔGint-145 kcal/mol
Surface area32100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.229, 107.229, 114.831
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-956-

HOH

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Components

#1: Protein Yeast 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 17% Peg 3350 100 mM Hepes, pH 7.5 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→53.63 Å / Num. obs: 67865 / % possible obs: 99.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.2
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.97 / Num. unique obs: 6573 / CC1/2: 0.715

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Processing

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

2ood


Resolution: 1.75→47.95 Å / SU ML: 0.1243 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.614
RfactorNum. reflection% reflection
Rfree0.1559 3440 5.07 %
Rwork0.1412 --
obs0.142 67865 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.63 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 91 436 4045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853718
X-RAY DIFFRACTIONf_angle_d1.10135040
X-RAY DIFFRACTIONf_chiral_restr0.0578576
X-RAY DIFFRACTIONf_plane_restr0.007637
X-RAY DIFFRACTIONf_dihedral_angle_d4.55393011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.22541280.2292541X-RAY DIFFRACTION99.96
1.77-1.80.22041130.19542556X-RAY DIFFRACTION100
1.8-1.830.21371180.18352579X-RAY DIFFRACTION99.93
1.83-1.850.19581260.1792534X-RAY DIFFRACTION100
1.85-1.890.20091010.1652579X-RAY DIFFRACTION99.93
1.89-1.920.18221410.16122549X-RAY DIFFRACTION100
1.92-1.950.20721450.16062517X-RAY DIFFRACTION100
1.95-1.990.1781360.15342559X-RAY DIFFRACTION100
1.99-2.030.1821480.14332531X-RAY DIFFRACTION100
2.03-2.070.1561510.14492524X-RAY DIFFRACTION100
2.07-2.120.19131390.13332568X-RAY DIFFRACTION99.96
2.12-2.180.17051380.132548X-RAY DIFFRACTION100
2.18-2.240.15351250.12752578X-RAY DIFFRACTION100
2.24-2.30.14361190.12742572X-RAY DIFFRACTION100
2.3-2.380.13841410.12312565X-RAY DIFFRACTION100
2.38-2.460.13981130.1212596X-RAY DIFFRACTION99.96
2.46-2.560.15931660.12342538X-RAY DIFFRACTION99.96
2.56-2.670.14481640.13222557X-RAY DIFFRACTION99.96
2.67-2.820.16171390.13882574X-RAY DIFFRACTION99.96
2.82-2.990.16761590.13942569X-RAY DIFFRACTION99.93
2.99-3.220.14641490.14382597X-RAY DIFFRACTION100
3.22-3.550.1431340.14042609X-RAY DIFFRACTION100
3.55-4.060.14011460.12922636X-RAY DIFFRACTION99.93
4.06-5.120.11261360.11632679X-RAY DIFFRACTION99.68
5.12-47.970.16671650.17842770X-RAY DIFFRACTION98.76
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0770952199-0.1040058836260.1393797880130.2211644768740.02382306310790.0250877823060.0404241327222-0.1873196844080.1114237399310.02287241668310.00824299230341-0.16120192854-0.00789678636490.483661255291-0.01859254692510.125586087847-0.0296503744715-0.004079269321180.507764940108-0.04068672951940.22256134898150.10396577158.8886653531722.5959114242
20.54355899576-0.2478741258170.1810989025830.460563735774-0.07163006315410.622375523270.006471029267380.09974240461690.0424057228729-0.0446562612198-0.0266797633541-0.0404114003805-0.1088859326860.1895133815350.02558301395430.107972053932-0.02619154241360.01739661704090.2147294372-0.003868614197590.14860259833926.700404404915.4391554082-0.869468209408
30.542490352552-0.06389654262340.09118867337550.2980482483-0.02335525229120.7061550301710.04347387470120.105527986505-0.0103857969343-0.0141524461672-0.0076986216411-0.03205973908880.03159945102560.218089176488-0.02836883992440.08194104344580.007737049756210.002106653685860.171270467703-0.02202911000540.13675019486726.81056645264.981072047934.80009550268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 79)
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 489 )

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