[English] 日本語
Yorodumi
- PDB-4x3n: Crystal structure of 34 kDa F-actin bundling protein from Dictyos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x3n
TitleCrystal structure of 34 kDa F-actin bundling protein from Dictyostelium discoideum
ComponentsCalcium-regulated actin-bundling protein
KeywordsPROTEIN BINDING / actin / cytoskeleton / bundling
Function / homology
Function and homology information


intranuclear rod / parallel actin filament bundle assembly / actin crosslink formation / cortical cytoskeleton / filamentous actin / pseudopodium / actin filament bundle assembly / phagocytic vesicle / filopodium / actin filament binding ...intranuclear rod / parallel actin filament bundle assembly / actin crosslink formation / cortical cytoskeleton / filamentous actin / pseudopodium / actin filament bundle assembly / phagocytic vesicle / filopodium / actin filament binding / calcium ion binding / cytoplasm
Similarity search - Function
Calcium-regulated actin-bundling protein, C-terminal / : / F actin bundling C terminal
Similarity search - Domain/homology
CITRIC ACID / Calcium-regulated actin-bundling protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å
AuthorsKim, M.-K. / Kim, J.-H. / Kim, J.-S. / Kang, S.-O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the 34 kDa F-actin-bundling protein ABP34 from Dictyostelium discoideum.
Authors: Kim, M.K. / Kim, J.H. / Kim, J.S. / Kang, S.O.
History
DepositionDec 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calcium-regulated actin-bundling protein
B: Calcium-regulated actin-bundling protein
C: Calcium-regulated actin-bundling protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5037
Polymers100,1913
Non-polymers3124
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.161, 85.244, 135.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Calcium-regulated actin-bundling protein / 34 kDa actin-binding protein


Mass: 33396.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: abpB, DDB_G0279081 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P24005
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: ammonium acetate, sodium citrate, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 12, 2010
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.89→72.19 Å / Num. obs: 72226 / % possible obs: 98.9 % / Redundancy: 9.6 % / Rsym value: 0.078 / Net I/σ(I): 34.5
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 5.4 % / % possible all: 88.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.89→72.19 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.686 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25237 3640 5 %RANDOM
Rwork0.20393 ---
obs0.20643 68586 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å20 Å2
2--1.61 Å20 Å2
3----1.14 Å2
Refinement stepCycle: 1 / Resolution: 1.89→72.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 16 383 6681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196436
X-RAY DIFFRACTIONr_bond_other_d0.0010.026062
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9588661
X-RAY DIFFRACTIONr_angle_other_deg0.89313995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92124.615325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.166151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1781533
X-RAY DIFFRACTIONr_chiral_restr0.110.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021507
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7643.2743082
X-RAY DIFFRACTIONr_mcbond_other2.7593.2743081
X-RAY DIFFRACTIONr_mcangle_it3.8884.8923842
X-RAY DIFFRACTIONr_mcangle_other3.8894.8933843
X-RAY DIFFRACTIONr_scbond_it3.5233.6033354
X-RAY DIFFRACTIONr_scbond_other3.5173.6023352
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3745.2434819
X-RAY DIFFRACTIONr_long_range_B_refined7.36430.64129000
X-RAY DIFFRACTIONr_long_range_B_other7.36430.63928997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 242 -
Rwork0.348 4772 -
obs--94.57 %

+
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