[English] 日本語
Yorodumi
- PDB-6atx: Crystal structure of Physcomitrella patens KAI2-like C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6atx
TitleCrystal structure of Physcomitrella patens KAI2-like C
ComponentsPpKAI2-like C
KeywordsHYDROLASE / alpha/beta hydrolase / strigolactone binding
Function / homologyAlpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74033790814 Å
AuthorsBurger, M. / Lee, H.J. / Chory, J.
CitationJournal: Cell Rep / Year: 2019
Title: Structural Basis of Karrikin and Non-natural Strigolactone Perception in Physcomitrella patens.
Authors: Burger, M. / Mashiguchi, K. / Lee, H.J. / Nakano, M. / Takemoto, K. / Seto, Y. / Yamaguchi, S. / Chory, J.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PpKAI2-like C


Theoretical massNumber of molelcules
Total (without water)30,4041
Polymers30,4041
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.630, 46.630, 140.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

-
Components

#1: Protein PpKAI2-like C


Mass: 30403.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens subsp. patens (plant)
Gene: PHYPADRAFT_213263 / Plasmid: pGEX4T3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9SKF7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.2 M ammonium sulfate, 0.2 M Bis-Tris, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2016 / Details: mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→46.63 Å / Num. obs: 7881 / % possible obs: 99.92 % / Redundancy: 13.7 % / Biso Wilson estimate: 37.0104001296 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2201 / Rpim(I) all: 0.06161 / Net I/σ(I): 12.35
Reflection shellResolution: 2.74→2.84 Å / Rmerge(I) obs: 0.8344 / CC1/2: 0.504 / Rpim(I) all: 0.2964

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IH1

4ih1


Resolution: 2.74033790814→46.63 Å / SU ML: 0.391600951074 / Cross valid method: FREE R-VALUE / σ(F): 1.35078110119 / Phase error: 22.6905586875
RfactorNum. reflection% reflection
Rfree0.219014953825 399 5.06280928816 %
Rwork0.177501886647 --
obs0.179600563238 7881 99.9365965001 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.3194246999 Å2
Refinement stepCycle: LAST / Resolution: 2.74033790814→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 0 42 2103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002860085055112111
X-RAY DIFFRACTIONf_angle_d0.5960300143512877
X-RAY DIFFRACTIONf_chiral_restr0.0440365621065334
X-RAY DIFFRACTIONf_plane_restr0.00358640620628369
X-RAY DIFFRACTIONf_dihedral_angle_d2.724639086741244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7403-3.13680.3142906916761360.2467411846022485X-RAY DIFFRACTION100
3.1368-3.95170.2156406996841270.1830745189982475X-RAY DIFFRACTION99.9615827891
3.9517-46.63670.1773657504091360.1441683703172522X-RAY DIFFRACTION99.8872604284

+
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