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- PDB-7r8z: Ancestral protein AncEn of Phosphomethylpyrimidine kinases family -

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Basic information

Entry
Database: PDB / ID: 7r8z
TitleAncestral protein AncEn of Phosphomethylpyrimidine kinases family
ComponentsPhosphomethylpyrimidine Kinase
KeywordsTRANSFERASE / ancestral protein reconstruction / 5-Phosphohydroxymethyl-2-methylpyrimidine kinase / Phosphomethylpyrimidine kinases family / enzyme evolution
Function / homologyBETA-MERCAPTOETHANOL / D(-)-TARTARIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMunoz, S. / Fuentes-Ugarte, N. / Maturana, P. / Gonzalez-Ordenes, F. / Cea, P. / Castro-Fernandez, V.
Funding support Chile, 3items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)1150460 Chile
Comision Nacional Cientifica y Technologica (CONICYT)3160332 Chile
Comision Nacional Cientifica y Technologica (CONICYT)EQM 120208 Chile
CitationJournal: To Be Published
Title: Ancestral protein AncEn of Phosphomethylpyrimidine Kinases family
Authors: Munoz, S. / Maturana, P. / Gonzalez-Ordenes, F. / Cea, P. / Castro-Fernandez, V.
History
DepositionJun 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_struct_assembly.details / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Atomic clashes
Details: The new model considerably reduces the clashscore value and includes a modification of two hydroxycysteine residues.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphomethylpyrimidine Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1384
Polymers30,7601
Non-polymers3783
Water79344
1
A: Phosphomethylpyrimidine Kinase
hetero molecules

A: Phosphomethylpyrimidine Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2768
Polymers61,5202
Non-polymers7576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area3470 Å2
ΔGint-13 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.451, 78.451, 142.973
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-442-

HOH

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Components

#1: Protein Phosphomethylpyrimidine Kinase


Mass: 30759.777 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-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.58 Å3/Da / Density % sol: 65.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein condition: Protein 20 mg/mL, HEPES 50 mM pH 8.0, NaCl 150 mM and 2-mercaptoethanol 5 mM Reservoir condition: Potassium sodium tartrate 0.8 M, Tris 0.1 M pH 8.0, PEG-MME 5000 0.5% v/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45867 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 5, 2019
RadiationMonochromator: Double Crystal Monochromator - Water-cooled Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45867 Å / Relative weight: 1
ReflectionResolution: 2.298→36.15 Å / Num. obs: 20580 / % possible obs: 99.77 % / Redundancy: 25 % / Biso Wilson estimate: 55.41 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.08904 / Rpim(I) all: 0.01809 / Rrim(I) all: 0.0909 / Net I/σ(I): 26.96
Reflection shellResolution: 2.298→2.38 Å / Rmerge(I) obs: 1.648 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 1984 / CC1/2: 0.826 / CC star: 0.951 / Rpim(I) all: 0.338 / Rrim(I) all: 1.683

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JXH

1jxh


Resolution: 2.3→36.15 Å / SU ML: 0.2632 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9365
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2236 1029 5 %
Rwork0.2036 19542 -
obs0.2046 20571 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 24 44 1704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231686
X-RAY DIFFRACTIONf_angle_d0.51782288
X-RAY DIFFRACTIONf_chiral_restr0.0431277
X-RAY DIFFRACTIONf_plane_restr0.0042298
X-RAY DIFFRACTIONf_dihedral_angle_d14.5043602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.26211420.25872685X-RAY DIFFRACTION98.85
2.42-2.570.28431440.22672732X-RAY DIFFRACTION100
2.57-2.770.2671450.24092755X-RAY DIFFRACTION100
2.77-3.050.3011450.23012765X-RAY DIFFRACTION100
3.05-3.490.26981470.22442797X-RAY DIFFRACTION100
3.49-4.390.22371490.18572821X-RAY DIFFRACTION100
4.39-36.150.17851570.18722987X-RAY DIFFRACTION99.68
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)
13.292993915070.361625634684-1.796509252772.68302046432-0.1336714971041.916151806390.141893047359-0.3821247509650.226857477548-0.1891793477410.03996436725870.0788369049507-0.286211621118-0.006711816039170.0001440875313980.3384018709880.02674114330040.01954033664420.549984614622-0.0161499765670.396637340736-10.80321590624.58291906491-10.2307410407
23.627768643441.45376668666-0.7727525889461.46513094991-0.3902597943751.115244173210.0015552891414-0.0713860537783-0.3629999503620.0579968101194-0.08343328519310.2442821366910.122868264734-0.589967420419-0.001122649987280.2805566156330.004646316374990.01382748459740.766712429987-0.02752301290590.496959774552-26.8237496552-5.01663446901-7.51251299576
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 97 )1 - 971 - 94
22chain 'A' and (resid 98 through 242 )98 - 24295 - 222

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