[English] 日本語
Yorodumi
- PDB-8pkr: Crystal structure of PknD-345, a repeat fragment from the M. tube... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pkr
TitleCrystal structure of PknD-345, a repeat fragment from the M. tuberculosis PknD beta-propeller
Componentsnon-specific serine/threonine protein kinase
KeywordsUNKNOWN FUNCTION / fragment / scaffold / beta propeller / globular / PknD
Function / homology
Function and homology information


regulation of primary metabolic process / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Protein kinase PknD, NHL repeat domain / NHL repeat profile. / NHL repeat / NHL repeat / Six-bladed beta-propeller, TolB-like / 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 kinase PknD, NHL repeat domain / NHL repeat profile. / NHL repeat / NHL repeat / Six-bladed beta-propeller, TolB-like / 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
Similarity search - Domain/homology
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsWouters, S.M.L.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S89918N Belgium
Research Foundation - Flanders (FWO)G0F9316N Belgium
Research Foundation - Flanders (FWO)G051917N Belgium
CitationJournal: To Be Published
Title: Computational design of the SAKe scaffold proteins
Authors: Wouters, S.M.L. / Noguchi, H. / Voet, A.R.D.
History
DepositionJun 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: non-specific serine/threonine protein kinase
B: non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3703
Polymers27,2782
Non-polymers921
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-24 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.701, 83.241, 83.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein non-specific serine/threonine protein kinase


Mass: 13638.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: pknD_1, pknD_2, ERS007657_00042, ERS007663_00011, ERS007665_00696, ERS007720_00884, SAMEA2683035_02262
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A045HV41, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.02 M Calcium chloride, 0.1 M Sodium acetate pH 4.6, 26% (v/v) MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.74999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.74999 Å / Relative weight: 1
ReflectionResolution: 0.95→41.73 Å / Num. obs: 142745 / % possible obs: 99.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 8.87 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.012 / Rrim(I) all: 0.045 / Net I/σ(I): 26.9 / Num. measured all: 1871882
Reflection shellResolution: 0.95→0.97 Å / % possible obs: 97.7 % / Redundancy: 13.4 % / Rmerge(I) obs: 1.223 / Num. measured all: 92378 / Num. unique obs: 6894 / CC1/2: 0.813 / Rpim(I) all: 0.342 / Rrim(I) all: 1.271 / Net I/σ(I) obs: 2.3

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→30.45 Å / SU ML: 0.0724 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.8557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1372 7091 4.97 %
Rwork0.1279 135549 -
obs0.1284 142640 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.86 Å2
Refinement stepCycle: LAST / Resolution: 0.95→30.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 6 235 2068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872024
X-RAY DIFFRACTIONf_angle_d1.12872811
X-RAY DIFFRACTIONf_chiral_restr0.0997339
X-RAY DIFFRACTIONf_plane_restr0.0089388
X-RAY DIFFRACTIONf_dihedral_angle_d12.2115717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.2212300.2234442X-RAY DIFFRACTION97.43
0.96-0.970.20852210.20594376X-RAY DIFFRACTION97.48
0.97-0.980.21372240.19014405X-RAY DIFFRACTION97.74
0.98-10.19642390.17924412X-RAY DIFFRACTION97.92
1-1.010.17592740.16184349X-RAY DIFFRACTION98.03
1.01-1.020.16432410.14244459X-RAY DIFFRACTION97.92
1.02-1.040.14172570.13414384X-RAY DIFFRACTION98.18
1.04-1.050.14082260.12954503X-RAY DIFFRACTION98.3
1.05-1.070.13842310.12464403X-RAY DIFFRACTION98.14
1.07-1.090.12642560.12344432X-RAY DIFFRACTION98.72
1.09-1.110.13572160.11584478X-RAY DIFFRACTION98.65
1.11-1.130.11052580.10534475X-RAY DIFFRACTION98.54
1.13-1.150.12582610.10264407X-RAY DIFFRACTION98.86
1.15-1.170.11062420.09744511X-RAY DIFFRACTION98.98
1.17-1.20.09712670.09874437X-RAY DIFFRACTION98.93
1.2-1.220.10711940.09694555X-RAY DIFFRACTION99.21
1.22-1.260.11552570.0984472X-RAY DIFFRACTION99.35
1.26-1.290.12072310.09994514X-RAY DIFFRACTION99.25
1.29-1.330.11072270.10424524X-RAY DIFFRACTION99.21
1.33-1.370.11262480.10614559X-RAY DIFFRACTION99.63
1.37-1.420.13492320.10484554X-RAY DIFFRACTION99.75
1.42-1.480.11842300.10864556X-RAY DIFFRACTION99.81
1.48-1.540.14752070.1084596X-RAY DIFFRACTION99.9
1.54-1.620.12661930.11114626X-RAY DIFFRACTION99.94
1.62-1.730.12562140.11874639X-RAY DIFFRACTION99.98
1.73-1.860.12092640.1254550X-RAY DIFFRACTION100
1.86-2.050.11432250.12194672X-RAY DIFFRACTION100
2.05-2.340.13122330.12674656X-RAY DIFFRACTION100
2.34-2.950.14772600.13944685X-RAY DIFFRACTION100
2.95-30.450.17092330.15664918X-RAY DIFFRACTION99.88

+
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