[English] 日本語
Yorodumi
- PDB-1ot3: Crystal structure of Drosophila deoxyribonucleotide kinase comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ot3
TitleCrystal structure of Drosophila deoxyribonucleotide kinase complexed with the substrate deoxythymidine
ComponentsDeoxyribonucleoside Kinase
KeywordsTRANSFERASE / protein-deoxynucleoside complex
Function / homology
Function and homology information


deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / uridine kinase activity / nucleoside salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / thymidine kinase activity / deoxyadenosine kinase activity ...deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / uridine kinase activity / nucleoside salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / thymidine kinase activity / deoxyadenosine kinase activity / cytidine kinase activity / DNA biosynthetic process / kinase activity / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Deoxynucleoside kinase / : / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE / Deoxynucleoside kinase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMikkelsen, N.E. / Johansson, K. / Karlsson, A. / Knecht, W. / Andersen, G. / Piskur, J. / Munch-Petersen, B. / Eklund, H.
CitationJournal: Biochemistry / Year: 2003
Title: Structural Basis for Feedback Inhibition of the Deoxyribonucleoside Salvage Pathway: Studies of the Drosophila Deoxyribonucleoside Kinase.
Authors: Mikkelsen, N.E. / Johansson, K. / Karlsson, A. / Knecht, W. / Andersen, G. / Piskur, J. / Munch-Petersen, B. / Eklund, H.
History
DepositionMar 21, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 28, 2014Group: Other
Revision 1.4Oct 25, 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_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Deoxyribonucleoside Kinase
B: Deoxyribonucleoside Kinase
C: Deoxyribonucleoside Kinase
D: Deoxyribonucleoside Kinase
E: Deoxyribonucleoside Kinase
F: Deoxyribonucleoside Kinase
G: Deoxyribonucleoside Kinase
H: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,82025
Polymers233,0188
Non-polymers2,80217
Water5,585310
1
A: Deoxyribonucleoside Kinase
B: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0277
Polymers58,2552
Non-polymers7735
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-57 kcal/mol
Surface area17800 Å2
MethodPISA
2
C: Deoxyribonucleoside Kinase
D: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9316
Polymers58,2552
Non-polymers6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-58 kcal/mol
Surface area17430 Å2
MethodPISA
3
E: Deoxyribonucleoside Kinase
F: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9316
Polymers58,2552
Non-polymers6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-59 kcal/mol
Surface area17410 Å2
MethodPISA
4
G: Deoxyribonucleoside Kinase
H: Deoxyribonucleoside Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9316
Polymers58,2552
Non-polymers6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-68 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.379, 71.158, 226.272
Angle α, β, γ (deg.)90.00, 90.59, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Deoxyribonucleoside Kinase / Dm-dNK


Mass: 29127.254 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9XZT6, deoxynucleoside kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.03 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, MPEG5000, PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MMES1reservoirpH6.5
20.2 Mammonium sulfate1reservoir
318-22 %(w/v)MPEG50001reservoir
45-10 %(w/v)PEG4001reservoir
55-10 mg/mlprotein1drop
65 mMdT1dropor dTTP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93927 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2002
RadiationMonochromator: DIAMOND CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 77914 / Num. obs: 70001 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 54.664 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.05 / Net I/σ(I): 8
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 1.8 / Num. unique all: 7680 / Rsym value: 0.236 / % possible all: 68.1
Reflection
*PLUS
Lowest resolution: 70 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Lowest resolution: 2.64 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.236

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J90

1j90


Resolution: 2.5→25 Å / σ(F): 1.8 / σ(I): 1.8 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 3560 -RANDOM
Rwork0.227 ---
all-77914 --
obs-70001 89.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.087 Å20 Å214.047 Å2
2---9.358 Å20 Å2
3---12.445 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12847 0 181 310 13338
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4921.5
X-RAY DIFFRACTIONc_mcangle_it2.5752
X-RAY DIFFRACTIONc_scbond_it1.9412
X-RAY DIFFRACTIONc_scangle_it2.9732.5
LS refinement shellResolution: 2.5→2.61 Å
RfactorNum. reflection
Rfree0.3843 304
Rwork0.3184 -
obs-6107
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5thm_xplor_paramthm_xplor_top
Refinement
*PLUS
Lowest resolution: 70 Å / Rfactor Rfree: 0.276
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d0.994

+
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