[English] 日本語
Yorodumi
- PDB-5hnv: Crystal structure of PpkA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hnv
TitleCrystal structure of PpkA
ComponentsPpkA N terminal
KeywordsTRANSFERASE / Kinase / complex / t6ss
Function / homology
Function and homology information


protein kinase activity / ATP binding
Similarity search - Function
Protein kinase 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
ADENOSINE-5'-TRIPHOSPHATE / PpkA N terminal
Similarity search - Component
Biological speciesSerratia sp. FS14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.41 Å
AuthorsLi, P.P. / Ran, T.T. / Wang, W.W.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31170686 China
National Natural Science Foundation of China31400055 China
National Natural Science Foundation of China31100028 China
the Natural Science Foundation of Jiangsu ProvinceBK20140690 China
CitationJournal: Biochem.J. / Year: 2018
Title: Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism.
Authors: Li, P.P. / Xu, D.Q. / Ma, T.Q. / Wang, D.Y. / Li, W.D. / He, J.H. / Ran, T.T. / Wang, W.W.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PpkA N terminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7364
Polymers34,1121
Non-polymers6243
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-2 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.753, 78.282, 59.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PpkA N terminal


Mass: 34112.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. FS14 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: A0A1S4NYE5*PLUS
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, HEPES, sodium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.41→20 Å / Num. obs: 59128 / % possible obs: 99.2 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 28.7
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 3.4 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.41→19.879 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2945 4.99 %Random selection
Rwork0.1827 ---
obs0.184 59070 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.41→19.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 38 267 2565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062369
X-RAY DIFFRACTIONf_angle_d0.963222
X-RAY DIFFRACTIONf_dihedral_angle_d23.67896
X-RAY DIFFRACTIONf_chiral_restr0.084348
X-RAY DIFFRACTIONf_plane_restr0.006420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4101-1.43320.2757950.27132268X-RAY DIFFRACTION85
1.4332-1.45790.29141480.2382661X-RAY DIFFRACTION100
1.4579-1.48440.24051450.23072630X-RAY DIFFRACTION100
1.4844-1.5130.26111380.22222670X-RAY DIFFRACTION100
1.513-1.54380.23711210.21892660X-RAY DIFFRACTION100
1.5438-1.57740.27721460.21842676X-RAY DIFFRACTION100
1.5774-1.61410.20861600.19652626X-RAY DIFFRACTION100
1.6141-1.65440.2441350.19432656X-RAY DIFFRACTION100
1.6544-1.69910.21151190.192716X-RAY DIFFRACTION100
1.6991-1.74910.20251490.1962647X-RAY DIFFRACTION100
1.7491-1.80550.20391530.19012667X-RAY DIFFRACTION100
1.8055-1.870.24681420.19372668X-RAY DIFFRACTION100
1.87-1.94480.22091370.18932672X-RAY DIFFRACTION100
1.9448-2.03320.22921460.18362694X-RAY DIFFRACTION100
2.0332-2.14030.20111500.18912685X-RAY DIFFRACTION100
2.1403-2.27420.21151410.18052717X-RAY DIFFRACTION100
2.2742-2.44950.21631340.18822708X-RAY DIFFRACTION100
2.4495-2.69550.20161240.18532744X-RAY DIFFRACTION100
2.6955-3.08430.20111460.18852717X-RAY DIFFRACTION100
3.0843-3.88120.20511560.16452756X-RAY DIFFRACTION100
3.8812-100.18781600.16212887X-RAY DIFFRACTION100

+
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