[English] 日本語
Yorodumi
- PDB-4esh: The crystal structure of thymidylate kinase from Pseudomonas aeru... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4esh
TitleThe crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with deoxythymidine.
ComponentsThymidylate kinase
KeywordsTRANSFERASE / thymidylate kinase / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
Function / homology
Function and homology information


dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytosol / cytoplasm
Similarity search - Function
Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE / Thymidylate kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with deoxythymidine.
Authors: Tan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6512
Polymers23,4091
Non-polymers2421
Water1,40578
1


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

A: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3024
Polymers46,8172
Non-polymers4842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3330 Å2
ΔGint-12 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.352, 55.352, 114.767
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsIt is predicted to be monomeric.

-
Components

#1: Protein Thymidylate kinase / / dTMP kinase


Mass: 23408.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2962, Pseudomonas aeruginosa, tmk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9HZN8, dTMP kinase
#2: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE / Thymidine


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8M Lithium Chloride, 0.1M Tris:HCl, 32% (w/v) PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.95→37 Å / Num. all: 15472 / Num. obs: 15472 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.9 / Num. unique all: 766 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E5U

4e5u


Resolution: 1.95→36.789 Å / SU ML: 0.49 / σ(F): 1.34 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 773 5.01 %Random
Rwork0.1816 ---
all0.1838 15434 --
obs0.1838 15434 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.038 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.672 Å2-0 Å2-0 Å2
2--2.672 Å20 Å2
3----5.3441 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 17 78 1699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071697
X-RAY DIFFRACTIONf_angle_d0.9962309
X-RAY DIFFRACTIONf_dihedral_angle_d12.958659
X-RAY DIFFRACTIONf_chiral_restr0.065259
X-RAY DIFFRACTIONf_plane_restr0.005313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.948-2.070.28651340.2182389X-RAY DIFFRACTION100
2.07-2.22980.21171230.1992407X-RAY DIFFRACTION100
2.2298-2.45420.28411360.18592422X-RAY DIFFRACTION100
2.4542-2.80920.26371170.20112445X-RAY DIFFRACTION100
2.8092-3.53880.22881470.182447X-RAY DIFFRACTION100
3.5388-36.79540.19351160.16892551X-RAY DIFFRACTION98
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)
16.4159-0.4012-1.24567.47780.43210.5173-0.0121-0.87430.4494-0.00770.5264-0.5282-0.1971.0869-0.420.22090.0072-0.04710.3777-0.02260.2811-26.446722.505919.0026
28.51142.20551.06061.87223.16129.132-0.15330.39791.1028-0.74440.1231-0.3976-1.66950.4210.07760.6007-0.0625-0.00630.30670.05860.51-18.727932.029719.1703
31.14331.10480.51955.77712.21842.47090.00790.07660.0207-0.06640.0886-0.3488-0.02940.2855-0.1570.1915-0.03090.01810.27930.02920.2508-16.67899.26917.5123
41.2022-0.02260.32462.64770.71212.3675-0.0119-0.0650.0056-0.08710.03660.0467-0.13560.0109-0.01960.2110.01030.01110.26820.01820.2414-28.673311.814217.2922
52.2702-2.39642.29417.4062-3.7965.203-0.0740.73380.62890.235-0.6117-1.2176-0.64211.57260.64460.5173-0.05630.09310.74120.07010.531-15.591912.75660.6995
64.1226-3.9113-4.87194.0543.64728.4099-0.19220.6895-0.3238-0.3672-0.37440.2285-0.3543-0.46210.53580.3321-0.0276-0.02640.28090.01070.2869-29.548215.51841.4902
78.13625.0088-2.22594.92-3.13234.9341-0.28660.30321.6479-0.95940.40120.5397-0.7405-0.3893-0.0810.60230.0335-0.02050.4245-0.01740.3613-31.165526.9168.3506
86.37860.6814-1.16657.3964-1.32744.9837-0.16230.61850.7199-1.25570.21981.4462-1.5442-1.10450.07680.79150.0378-0.29870.4290.01270.9287-27.812134.856216.4009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:15)A-1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resseq 16:30)A16 - 30
3X-RAY DIFFRACTION3chain 'A' and (resseq 31:62)A31 - 62
4X-RAY DIFFRACTION4chain 'A' and (resseq 63:136)A63 - 136
5X-RAY DIFFRACTION5chain 'A' and (resseq 137:159)A137 - 159
6X-RAY DIFFRACTION6chain 'A' and (resseq 160:176)A160 - 176
7X-RAY DIFFRACTION7chain 'A' and (resseq 177:189)A177 - 189
8X-RAY DIFFRACTION8chain 'A' and (resseq 190:209)A190 - 209

+
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