[English] 日本語
Yorodumi
- PDB-3q2b: Crystal Structure of an Actin Depolymerizing Factor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q2b
TitleCrystal Structure of an Actin Depolymerizing Factor
ComponentsCofilin/actin-depolymerizing factor homolog 1
KeywordsActin-BINDING PROTEIN / Actin Regulator / Actin
Function / homology
Function and homology information


cytoplasmic actin-based contraction involved in cell motility / actin filament depolymerization / actin monomer binding / actin cytoskeleton / actin cytoskeleton organization / cytoplasm
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / D(-)-TARTARIC ACID / Cofilin/actin-depolymerizing factor homolog 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWong, W. / Clarke, O.B. / Gulbis, J.M. / Baum, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Minimal requirements for actin filament disassembly revealed by structural analysis of malaria parasite actin-depolymerizing factor 1
Authors: Wong, W. / Skau, C.T. / Marapana, D.S. / Hanssen, E. / Taylor, N.L. / Riglar, D.T. / Zuccala, E.S. / Angrisano, F. / Lewis, H. / Catimel, B. / Clarke, O.B. / Kershaw, N.J. / Perugini, M.A. / ...Authors: Wong, W. / Skau, C.T. / Marapana, D.S. / Hanssen, E. / Taylor, N.L. / Riglar, D.T. / Zuccala, E.S. / Angrisano, F. / Lewis, H. / Catimel, B. / Clarke, O.B. / Kershaw, N.J. / Perugini, M.A. / Kovar, D.R. / Gulbis, J.M. / Baum, J.
History
DepositionDec 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cofilin/actin-depolymerizing factor homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3575
Polymers13,9011
Non-polymers4564
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.970, 38.970, 142.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Cofilin/actin-depolymerizing factor homolog 1 / PfADF1


Mass: 13900.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: HB3 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P86292
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1.94 Å3/Da / Density % sol: 36.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8M (NH4)2SO4, 0.2M KNa tartrate, 0.1M NaOAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.6→27.6 Å / Num. all: 16000 / Num. obs: 15439 / % possible obs: 80 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 3.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1494 / % possible all: 80

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F7S

1f7s


Resolution: 1.6→27.556 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8501 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 767 4.99 %
Rwork0.1928 --
obs0.1942 15356 99.82 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.587 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 100.5 Å2 / Biso mean: 30.2127 Å2 / Biso min: 13.57 Å2
Baniso -1Baniso -2Baniso -3
1-3.5578 Å20 Å2-0 Å2
2--3.5578 Å2-0 Å2
3----7.1155 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 26 77 1030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091023
X-RAY DIFFRACTIONf_angle_d1.2031387
X-RAY DIFFRACTIONf_chiral_restr0.082167
X-RAY DIFFRACTIONf_plane_restr0.005180
X-RAY DIFFRACTIONf_dihedral_angle_d15.554391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5995-1.7230.28971350.254428632998
1.723-1.89640.27081610.222328262987
1.8964-2.17070.21071680.179228713039
2.1707-2.73440.2221380.181629273065
2.7344-27.560.2061650.190631023267
Refinement TLS params.Method: refined / Origin x: 5.649 Å / Origin y: 16.3572 Å / Origin z: 9.9892 Å
111213212223313233
T0.1845 Å2-0.0015 Å20.0227 Å2-0.0876 Å2-0.0029 Å2--0.135 Å2
L1.3209 °20.0119 °2-0.4469 °2-0.8355 °20.4601 °2--2.2692 °2
S0.1517 Å °0.0601 Å °0.0387 Å °-0.0249 Å °-0.0464 Å °-0.0334 Å °-0.3269 Å °0.0769 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 121
2X-RAY DIFFRACTION1allA1 - 203
3X-RAY DIFFRACTION1allA1 - 123
4X-RAY DIFFRACTION1allA1 - 124
5X-RAY DIFFRACTION1allA1 - 125
6X-RAY DIFFRACTION1allA1 - 126

+
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