[English] 日本語
Yorodumi
- PDB-3d5u: Crystal structure of a wildtype Polo-like kinase 1 (Plk1) catalyt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d5u
TitleCrystal structure of a wildtype Polo-like kinase 1 (Plk1) catalytic domain.
ComponentsPolo-like kinase 1
KeywordsTRANSFERASE / Polo-like kinase 1 / Plk1 / catalytic domain / small-molecule inhibitor / Kinase
Function / homology
Function and homology information


Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / Regulation of PLK1 Activity at G2/M Transition / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / EML4 and NUDC in mitotic spindle formation / Polo-like kinase mediated events / Cyclin A/B1/B2 associated events during G2/M transition / The role of GTSE1 in G2/M progression after G2 checkpoint ...Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / Regulation of PLK1 Activity at G2/M Transition / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / EML4 and NUDC in mitotic spindle formation / Polo-like kinase mediated events / Cyclin A/B1/B2 associated events during G2/M transition / The role of GTSE1 in G2/M progression after G2 checkpoint / polo kinase / mitotic spindle organization / kinetochore / spindle pole / mitotic cell cycle / retina development in camera-type eye / midbody / cell division / protein serine/threonine kinase activity / centrosome / ATP binding / nucleus / cytoplasm
Similarity search - Function
Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK / Serine/threonine-protein kinase PLK
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsElling, R.A. / Fucini, R.V. / Romanowski, M.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of the wild-type and activated catalytic domains of Brachydanio rerio Polo-like kinase 1 (Plk1): changes in the active-site conformation and interactions with ligands.
Authors: Elling, R.A. / Fucini, R.V. / Romanowski, M.J.
History
DepositionMay 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polo-like kinase 1


Theoretical massNumber of molelcules
Total (without water)35,9791
Polymers35,9791
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.841, 135.841, 135.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

-
Components

#1: Protein Polo-like kinase 1


Mass: 35978.969 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: plk1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star
References: UniProt: Q4KMI8, UniProt: Q6DRK7*PLUS, polo kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M tri-sodium citrate pH 5.6, 0.2 M (NH4) ...Details: hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M tri-sodium citrate pH 5.6, 0.2 M (NH4)2SO4, and 25% PEG 3350; cryoprotectant: paraffin oil., VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2007
RadiationMonochromator: Side-scattering cube root I-beam bent single crystal; asymmetric cut 12.2 degs. Crystal type: Si(311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 9961 / % possible obs: 96.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.4
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3d5w

3d5w


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.878 / SU B: 17.431 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28127 988 9.9 %RANDOM
Rwork0.22543 ---
obs0.23105 8970 95.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.537 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 0 29 2329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222353
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8231.983180
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8485287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93622.718103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82415424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8681520
X-RAY DIFFRACTIONr_chiral_restr0.0520.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1610.21030
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21616
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2682.51484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.252342
X-RAY DIFFRACTIONr_scbond_it0.882.5966
X-RAY DIFFRACTIONr_scangle_it1.5025838
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.898 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.328 86 -
Rwork0.325 883 -
obs--97.58 %

+
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