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- PDB-5yox: HD domain-containing protein YGK1(YGL101W) -

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Basic information

Entry
Database: PDB / ID: 5yox
TitleHD domain-containing protein YGK1(YGL101W)
ComponentsHD domain-containing protein YGL101W
KeywordsLYASE / HD domain / Zn / Saccharomyces cerevisiae
Function / homology
Function and homology information


deoxyribonucleoside monophosphate catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / GMP 5'-nucleotidase activity / nucleus / metal ion binding / cytoplasm
Similarity search - Function
HD domain / 5'-deoxynucleotidase YfbR/HDDC2 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
5'-deoxynucleotidase YGK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsYang, J. / Wang, F. / Gao, Z. / Zhou, K. / Liu, Q.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: HD domain-containing protein YGK1(YGL101W)
Authors: Yang, J. / Wang, F. / Zhou, K. / Gao, Z. / Liu, Q.
History
DepositionOct 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HD domain-containing protein YGL101W
B: HD domain-containing protein YGL101W
C: HD domain-containing protein YGL101W
D: HD domain-containing protein YGL101W
E: HD domain-containing protein YGL101W
F: HD domain-containing protein YGL101W
G: HD domain-containing protein YGL101W
H: HD domain-containing protein YGL101W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,43816
Polymers204,9158
Non-polymers5238
Water2,828157
1
A: HD domain-containing protein YGL101W
G: HD domain-containing protein YGL101W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3604
Polymers51,2292
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-100 kcal/mol
Surface area16990 Å2
MethodPISA
2
B: HD domain-containing protein YGL101W
C: HD domain-containing protein YGL101W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3604
Polymers51,2292
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-102 kcal/mol
Surface area16890 Å2
MethodPISA
3
D: HD domain-containing protein YGL101W
H: HD domain-containing protein YGL101W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3604
Polymers51,2292
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-103 kcal/mol
Surface area17400 Å2
MethodPISA
4
E: HD domain-containing protein YGL101W
F: HD domain-containing protein YGL101W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3604
Polymers51,2292
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-100 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.633, 142.178, 112.266
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HD domain-containing protein YGL101W


Mass: 25614.383 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YGL101W / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53144
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 4.5
Details: 0.1M Sodium Acetate pH 4.5 22%(w/v) PEG3350 1mM CdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.6→30 Å / Num. obs: 49334 / % possible obs: 98.4 % / Redundancy: 3.7 % / Net I/σ(I): 16.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3 % / % possible all: 86.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
SHELXCDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→24.77 Å / Cross valid method: FREE R-VALUE / σ(F): 57.66 / Phase error: 28.55
RfactorNum. reflection% reflection
Rfree0.245 2528 5.13 %
Rwork0.207 --
obs0.214 49323 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.94 Å2
Refinement stepCycle: LAST / Resolution: 2.61→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11754 0 8 157 11919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01512002
X-RAY DIFFRACTIONf_angle_d1.08216081
X-RAY DIFFRACTIONf_dihedral_angle_d22.7754601
X-RAY DIFFRACTIONf_chiral_restr0.0631767
X-RAY DIFFRACTIONf_plane_restr0.0052032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6092-2.65930.33721150.31362213X-RAY DIFFRACTION79
2.6593-2.71350.36791230.30552433X-RAY DIFFRACTION89
2.7135-2.77240.32791540.29972554X-RAY DIFFRACTION90
2.7724-2.83680.31661320.28782557X-RAY DIFFRACTION94
2.8368-2.90760.33581810.28362625X-RAY DIFFRACTION93
2.9076-2.98610.3361450.27722603X-RAY DIFFRACTION95
2.9861-3.07380.32241340.26682659X-RAY DIFFRACTION95
3.0738-3.17280.23971430.26532633X-RAY DIFFRACTION95
3.1728-3.28590.27471260.24232675X-RAY DIFFRACTION95
3.2859-3.41710.29571460.24052577X-RAY DIFFRACTION95
3.4171-3.57210.26051510.21692652X-RAY DIFFRACTION95
3.5721-3.75970.23931200.19812708X-RAY DIFFRACTION96
3.7597-3.99420.21731250.19132612X-RAY DIFFRACTION95
3.9942-4.30080.22641540.18662646X-RAY DIFFRACTION94
4.3008-4.73040.18631460.16342643X-RAY DIFFRACTION95
4.7304-5.40770.1981480.17032645X-RAY DIFFRACTION95
5.4077-6.78580.25711310.20992675X-RAY DIFFRACTION95
6.7858-23.49920.20231360.1742676X-RAY DIFFRACTION94

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