[English] 日本語
Yorodumi
- PDB-4dix: Crystal structure of the Ig-PH domain of actin-binding protein SCAB1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dix
TitleCrystal structure of the Ig-PH domain of actin-binding protein SCAB1
ComponentsPlectin-related protein
KeywordsPROTEIN BINDING / PH domain / Ig domain / malonate ion / beta sheet / PH superfold / cytosolic
Function / homology
Function and homology information


regulation of stomatal movement / actin filament organization / actin binding / cytoskeleton / cytoplasm
Similarity search - Function
PH-domain like - #140 / Immunoglobulin-like - #2700 / Stomatal closure-related actin-binding protein, coiled-coil domain / Stomatal closure-related actin-binding protein, actin-binding domain / Stomatal closure-related actin-binding protein / Stomatal closure-related actin-binding protein, PH domain / Ig domain of plant-specific actin-binding protein / Actin-binding domain of plant-specific actin-binding protein / Coiled-coil regions of plant-specific actin-binding protein / PH domain of plant-specific actin-binding protein ...PH-domain like - #140 / Immunoglobulin-like - #2700 / Stomatal closure-related actin-binding protein, coiled-coil domain / Stomatal closure-related actin-binding protein, actin-binding domain / Stomatal closure-related actin-binding protein / Stomatal closure-related actin-binding protein, PH domain / Ig domain of plant-specific actin-binding protein / Actin-binding domain of plant-specific actin-binding protein / Coiled-coil regions of plant-specific actin-binding protein / PH domain of plant-specific actin-binding protein / PH-domain like / Roll / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
MALONATE ION / Stomatal closure-related actin-binding protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 Å
AuthorsZhang, W. / Ye, K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Plant actin-binding protein SCAB1 is dimeric actin cross-linker with atypical pleckstrin homology domain
Authors: Zhang, W. / Zhao, Y. / Guo, Y. / Ye, K.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Plectin-related protein
B: Plectin-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9524
Polymers49,7482
Non-polymers2042
Water6,666370
1
A: Plectin-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9762
Polymers24,8741
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plectin-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9762
Polymers24,8741
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.329, 76.329, 161.856
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-766-

HOH

21B-696-

HOH

31B-725-

HOH

-
Components

#1: Protein Plectin-related protein / Putative uncharacterized protein At2g26770


Mass: 24874.062 Da / Num. of mol.: 2 / Fragment: Ig-PH domain, UNP RESIDUES 272-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g26770, AT2G26770 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O48791
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.74 Å3/Da / Density % sol: 55.04 % / Mosaicity: 0.327 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2.0M sodium malonate, pH 6.4, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 20, 2008
RadiationMonochromator: CuK / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 58454 / % possible obs: 95.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.05 / Χ2: 1.183 / Net I/σ(I): 19.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.7310.50.56527581.086192.8
1.73-1.7610.90.46227861.117192.9
1.76-1.7910.90.37428001.132193.4
1.79-1.83110.32728231.163193.7
1.83-1.87110.27428641.173194.1
1.87-1.91110.23128131.245194.3
1.91-1.96110.18628691.263194.8
1.96-2.02110.15128551.246194.8
2.02-2.07110.12128661.285195.3
2.07-2.14110.10228981.271195.8
2.14-2.22110.09529161.279195.7
2.22-2.3110.90.08528961.431196.5
2.31-2.41110.07129321.248196.5
2.41-2.5410.90.06529881.247197.1
2.54-2.710.90.05629691.232197.4
2.7-2.910.80.04929691.166197.9
2.9-3.210.70.04130471.098198.2
3.2-3.6610.40.03730511.059198.6
3.66-4.610.20.03430940.973198.9
4.6-209.50.03232600.913198.9

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
DENZOdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.904 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2993 5.1 %RANDOM
Rwork0.2068 ---
obs0.2081 58426 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.94 Å2 / Biso mean: 27.1781 Å2 / Biso min: 13.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 14 370 3602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193306
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9594469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57523.577137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19815564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4851522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212486
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 211 -
Rwork0.371 3660 -
all-3871 -
obs--92.52 %

+
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