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- PDB-7l07: Last common ancestor of HMPPK and PLK/HMPPK vitamin kinases -

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Basic information

Entry
Database: PDB / ID: 7l07
TitleLast common ancestor of HMPPK and PLK/HMPPK vitamin kinases
ComponentsAncestral Protein AncCAncestor
KeywordsTRANSFERASE / Ancestral sequence reconstruction / Hydroxymethylpyrimidine Kinase / Pyridoxal Kinase
Function / homologyALUMINUM FLUORIDE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGonzalez-Ordenes, F. / Maturana, P. / Herrera-Morande, A. / Araya, G. / Arizabalos, S. / Castro-Fernandez, V.
Funding support Chile, 3items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)170497 Chile
Comision Nacional Cientifica y Technologica (CONICYT)1150460 Chile
Comision Nacional Cientifica y Technologica (CONICYT)11181133 Chile
CitationJournal: Protein Sci. / Year: 2021
Title: Crystal structure and molecular dynamics simulations of a promiscuous ancestor reveal residues and an epistatic interaction involved in substrate binding and catalysis in the ATP-dependent ...Title: Crystal structure and molecular dynamics simulations of a promiscuous ancestor reveal residues and an epistatic interaction involved in substrate binding and catalysis in the ATP-dependent vitamin kinase family members.
Authors: Gonzalez-Ordenes, F. / Bravo-Moraga, F. / Gonzalez, E. / Hernandez-Cabello, L. / Alzate-Morales, J. / Guixe, V. / Castro-Fernandez, V.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 18, 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

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Assembly

Deposited unit
A: Ancestral Protein AncC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3184
Polymers30,0661
Non-polymers2523
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ancestral Protein AncC
hetero molecules

A: Ancestral Protein AncC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6368
Polymers60,1322
Non-polymers5046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area2930 Å2
ΔGint-10 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.644, 65.644, 243.726
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

#1: Protein Ancestral Protein AncC / Ancestor


Mass: 30066.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: hydroxymethylpyrimidine kinase
#2: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 20 mM tris 7.8, 10 mM MgCl, 10 mM ADP, 1 mM AlCl3 and 30 mM NaF. Crystalization condition: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.0 and 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45854 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45854 Å / Relative weight: 1
ReflectionResolution: 2→46.58 Å / Num. obs: 22065 / % possible obs: 99.91 % / Redundancy: 10.9 % / Biso Wilson estimate: 25.56 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1453 / Rpim(I) all: 0.04585 / Rrim(I) all: 0.1525 / Net I/av σ(I): 13.52 / Net I/σ(I): 13.52
Reflection shellResolution: 2→2.072 Å / Redundancy: 10 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2142 / CC1/2: 0.793 / CC star: 0.94 / Rpim(I) all: 0.3518 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDS1data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C5K

4c5k


Resolution: 2→46.58 Å / SU ML: 0.2249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8206
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2152 1065 4.83 %
Rwork0.2075 20987 -
obs0.2079 22052 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.22 Å2
Refinement stepCycle: LAST / Resolution: 2→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1583 0 12 122 1717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671626
X-RAY DIFFRACTIONf_angle_d1.01732199
X-RAY DIFFRACTIONf_chiral_restr0.0614272
X-RAY DIFFRACTIONf_plane_restr0.005277
X-RAY DIFFRACTIONf_dihedral_angle_d19.7855586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.34491350.26952531X-RAY DIFFRACTION99.89
2.09-2.20.2161310.2212557X-RAY DIFFRACTION99.93
2.2-2.340.20371160.21272578X-RAY DIFFRACTION99.93
2.34-2.520.23351250.20052582X-RAY DIFFRACTION100
2.52-2.770.21441380.19442580X-RAY DIFFRACTION100
2.77-3.170.20021280.19572629X-RAY DIFFRACTION100
3.18-40.20761460.18142651X-RAY DIFFRACTION100
4-46.580.2041460.22422879X-RAY DIFFRACTION99.74

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