[English] 日本語
Yorodumi
- PDB-1d0n: THE CRYSTAL STRUCTURE OF CALCIUM-FREE EQUINE PLASMA GELSOLIN. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d0n
TitleTHE CRYSTAL STRUCTURE OF CALCIUM-FREE EQUINE PLASMA GELSOLIN.
ComponentsHORSE PLASMA GELSOLIN
KeywordsCONTRACTILE PROTEIN / MIXED ALPHA-BETA STRUCTURE / ACTIN-BINDING PROTEIN / PROTEIN DOMAIN PACKING
Function / homology
Function and homology information


actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / cilium assembly / phosphatidylinositol-4,5-bisphosphate binding / central nervous system development / actin filament binding / actin cytoskeleton / extracellular space ...actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / cilium assembly / phosphatidylinositol-4,5-bisphosphate binding / central nervous system development / actin filament binding / actin cytoskeleton / extracellular space / metal ion binding / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsBurtnick, L.D. / Robinson, R. / Li, C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: The crystal structure of plasma gelsolin: implications for actin severing, capping, and nucleation.
Authors: Burtnick, L.D. / Koepf, E.K. / Grimes, J. / Jones, E.Y. / Stuart, D.I. / McLaughlin, P.J. / Robinson, R.C.
History
DepositionSep 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HORSE PLASMA GELSOLIN
B: HORSE PLASMA GELSOLIN


Theoretical massNumber of molelcules
Total (without water)161,3832
Polymers161,3832
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: HORSE PLASMA GELSOLIN
B: HORSE PLASMA GELSOLIN

A: HORSE PLASMA GELSOLIN
B: HORSE PLASMA GELSOLIN

A: HORSE PLASMA GELSOLIN
B: HORSE PLASMA GELSOLIN

A: HORSE PLASMA GELSOLIN
B: HORSE PLASMA GELSOLIN


Theoretical massNumber of molelcules
Total (without water)645,5328
Polymers645,5328
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area22990 Å2
ΔGint-101 kcal/mol
Surface area237440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.400, 169.400, 154.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein HORSE PLASMA GELSOLIN


Mass: 80691.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Tissue: PLASMA / References: UniProt: Q28372
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: ammonium sulfate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
134 %satammonium sulfate1reservoir
2100 mMTris-HCl1reservoirpH8.0
310 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 14, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 71395 / Num. obs: 65683 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.44 % / Biso Wilson estimate: 22.81 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 23.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.12 % / Rmerge(I) obs: 0.246 / Num. unique all: 6242 / % possible all: 82

-
Processing

Software
NameVersionClassification
CNSrefinement
SCALEPACKdata scaling
SHELXSphasing
X-PLOR& CNSrefinement
DENZOdata reduction
RefinementResolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 3617 -RANDOM
Rwork0.2049 ---
all0.2116 71395 --
obs0.2116 65683 92 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11382 0 0 284 11666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.339
Software
*PLUS
Name: 'X-PLOR & CNS' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg

+
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