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- PDB-8g1h: Ancestral protein AncTh of Phosphomethylpirimidine kinases family -

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Basic information

Entry
Database: PDB / ID: 8g1h
TitleAncestral protein AncTh of Phosphomethylpirimidine kinases family
ComponentsPhosphomethylpyrimidine Kinase
KeywordsTRANSFERASE / Ancestral protein reconstruction / 5-phosphohydroxymethyl-2-methylpirimidine kinase / phosphomethylpirimidine kinases family / enzyme evolution
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPerez, M. / Munoz, S. / Cea, P. / Castro-Fernandez, V.
Funding support Chile, 2items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)1221667 Chile
Comision Nacional Cientifica y Technologica (CONICYT)EQM 120208 Chile
CitationJournal: To Be Published
Title: Ancestral protein AncTh of Phosphomethylpyrimidine kinases
Authors: Perez, M. / Munoz, S. / Cea, P. / Castro-Fernandez, V.
History
DepositionFeb 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphomethylpyrimidine Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1135
Polymers26,7991
Non-polymers3144
Water48627
1
A: Phosphomethylpyrimidine Kinase
hetero molecules

A: Phosphomethylpyrimidine Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,22610
Polymers53,5982
Non-polymers6288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5030 Å2
ΔGint-50 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.410, 59.410, 254.936
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Phosphomethylpyrimidine Kinase


Mass: 26798.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: phosphooxymethylpyrimidine kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein conditions: Protein 26 mg/ml, Tris-HCl 25 mM, NaCl 0.3 M, b-Mercaptoethanol 5 mM, ATP 1 mM, MgCl2 5 mM. Reservoir condition: Ethylene glycols 0.12 M (0.3M Diethylene glycol; 0.3M ...Details: Protein conditions: Protein 26 mg/ml, Tris-HCl 25 mM, NaCl 0.3 M, b-Mercaptoethanol 5 mM, ATP 1 mM, MgCl2 5 mM. Reservoir condition: Ethylene glycols 0.12 M (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), Sodium HEPES/ MOPS pH 7.5, 37.5% precipitants (MPD, PEG 1000, PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 7, 2022
RadiationMonochromator: Double crystal Monochromator - water- cooled Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 2.7→44.01 Å / Num. obs: 8030 / % possible obs: 99.84 % / Redundancy: 34.1 % / Biso Wilson estimate: 54.5 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1926 / Rpim(I) all: 0.033 / Rrim(I) all: 0.1956 / Net I/av σ(I): 21.62 / Net I/σ(I): 21.62
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 1.275 / Mean I/σ(I) obs: 4.05 / Num. unique obs: 753 / CC1/2: 0.94 / CC star: 0.984 / Rpim(I) all: 0.2123 / Rrim(I) all: 1.293 / % possible all: 99.87

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UB0

1ub0


Resolution: 2.7→44.01 Å / SU ML: 0.3315 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.025
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2285 461 5.75 %
Rwork0.2019 7562 -
obs0.2035 8023 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 18 27 1930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461929
X-RAY DIFFRACTIONf_angle_d0.73142622
X-RAY DIFFRACTIONf_chiral_restr0.0495316
X-RAY DIFFRACTIONf_plane_restr0.0063342
X-RAY DIFFRACTIONf_dihedral_angle_d11.9686701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.090.29951550.23262409X-RAY DIFFRACTION99.92
3.09-3.890.2781420.21342479X-RAY DIFFRACTION99.85
3.89-44.010.18741640.18832674X-RAY DIFFRACTION99.86

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