[English] 日本語
Yorodumi
- PDB-8g1h: Ancestral protein AncTh of Phosphomethylpirimidine kinases family -

+
Open data


ID or keywords:

Loading...

-
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: Mol.Biol.Evol. / Year: 2024
Title: Deciphering Structural Traits for Thermal and Kinetic Stability across Protein Family Evolution through Ancestral Sequence Reconstruction.
Authors: Cea, P.A. / Perez, M. / Herrera, S.M. / Munoz, S.M. / Fuentes-Ugarte, N. / Coche-Miranda, J. / Maturana, P. / Guixe, V. / Castro-Fernandez, V.
History
DepositionFeb 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more