[English] 日本語
Yorodumi
- PDB-6iqi: crystal structure of Arabidopsis thaliana Profilin 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iqi
Titlecrystal structure of Arabidopsis thaliana Profilin 2
ComponentsProfilin-2
KeywordsPLANT PROTEIN / actin binding / regulate actin network
Function / homology
Function and homology information


inflorescence development / lateral root development / leaf development / actin polymerization or depolymerization / chloroplast / defense response / actin binding / cytoskeleton / endoplasmic reticulum / nucleus ...inflorescence development / lateral root development / leaf development / actin polymerization or depolymerization / chloroplast / defense response / actin binding / cytoskeleton / endoplasmic reticulum / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsQiao, Z. / Gao, Y.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore) Singapore
Citation
Journal: J.Biol.Chem. / Year: 2019
Title: Structural and computational examination of theArabidopsisprofilin-Poly-P complex reveals mechanistic details in profilin-regulated actin assembly.
Authors: Qiao, Z. / Sun, H. / Ng, J.T.Y. / Ma, Q. / Koh, S.H. / Mu, Y. / Miao, Y. / Gao, Y.G.
#1: Journal: To Be Published
Title: Arabidopsis Profilin2
Authors: Qiao, Z. / Gao, Y.
History
DepositionNov 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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: Profilin-2
B: Profilin-2


Theoretical massNumber of molelcules
Total (without water)28,0222
Polymers28,0222
Non-polymers00
Water1267
1
A: Profilin-2


Theoretical massNumber of molelcules
Total (without water)14,0111
Polymers14,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Profilin-2


Theoretical massNumber of molelcules
Total (without water)14,0111
Polymers14,0111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.680, 58.680, 83.938
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32

-
Components

#1: Protein Profilin-2


Mass: 14010.833 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRO2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q42418
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 291.15 K / Method: evaporation
Details: 0.1M Tris HCl (pH 8.5), 2.2M ammonium phosphate dibasic

-
Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→32.36 Å / Num. obs: 19448 / % possible obs: 98.91 % / Redundancy: 4.2 % / CC1/2: 0.996 / Net I/σ(I): 6
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 719 / CC1/2: 0.6

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NUL

3nul


Resolution: 2.4→27.7 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2967 1168 -RANDOM
Rwork0.2623 ---
obs0.2656 12569 99.12 %-
Displacement parametersBiso mean: 64.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 0 7 1965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562000
X-RAY DIFFRACTIONf_angle_d0.91972704
X-RAY DIFFRACTIONf_chiral_restr0.0548291
X-RAY DIFFRACTIONf_plane_restr0.005355
X-RAY DIFFRACTIONf_dihedral_angle_d17.57561158
LS refinement shellResolution: 2.4→2.48 Å
RfactorNum. reflection% reflection
Rfree0.4503 --
Rwork0.3891 --
obs-1274 100 %

+
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