[English] 日本語
Yorodumi
- PDB-6a6y: Crystal Structure of Asf1 from Plasmodium falciparum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a6y
TitleCrystal Structure of Asf1 from Plasmodium falciparum
ComponentsHistone chaperone ASF1, putative
KeywordsCHAPERONE / Histone chaperone / Chromatin assembly and disassembly / Plasmodium facliparum
Function / homology
Function and homology information


chromatin organization => GO:0006325 / : / chromatin organization => GO:0006325 / : / chromatin => GO:0000785 / DNA replication-dependent chromatin assembly / nucleosome disassembly / unfolded protein binding / histone binding / chromatin binding
Similarity search - Function
Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Histone chaperone ASF1, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.491 Å
AuthorsSrivastava, D.K. / Roy, S.
CitationJournal: To Be Published
Title: Structural and Functional characterization of As1 from Plasmodium falciparum
Authors: Srivastava, D.K. / Gunjan, S. / Seshadri, V. / Roy, S.
History
DepositionJun 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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: Histone chaperone ASF1, putative
B: Histone chaperone ASF1, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,90110
Polymers37,4292
Non-polymers4738
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-23 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.733, 62.733, 98.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Histone chaperone ASF1, putative


Mass: 18714.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1224500 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I5H2
#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 3350, 0.2M Sodium thiocyanate, 0.1M MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 25, 2014 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.491→44.36 Å / Num. obs: 13132 / % possible obs: 97.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 41.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1232 / Rpim(I) all: 0.04838 / Rrim(I) all: 0.1324 / Net I/σ(I): 13.86
Reflection shellResolution: 2.491→2.58 Å / Redundancy: 7.3 % / Num. unique obs: 1258 / CC1/2: 0.831 / % possible all: 95.66

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HUE

2hue


Resolution: 2.491→44.359 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.76
RfactorNum. reflection% reflection
Rfree0.2149 707 5.39 %
Rwork0.192 --
obs0.1933 13105 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.491→44.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 26 129 2653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032576
X-RAY DIFFRACTIONf_angle_d0.5793481
X-RAY DIFFRACTIONf_dihedral_angle_d4.6141549
X-RAY DIFFRACTIONf_chiral_restr0.053381
X-RAY DIFFRACTIONf_plane_restr0.004448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4914-2.68380.2891330.26082429X-RAY DIFFRACTION96
2.6838-2.95380.29891340.24792465X-RAY DIFFRACTION97
2.9538-3.38110.23171430.2182471X-RAY DIFFRACTION98
3.3811-4.25930.20681610.17742473X-RAY DIFFRACTION98
4.2593-44.36590.17021360.15782560X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0122-0.6582-0.18714.15750.20954.07270.0712-0.1085-0.2674-0.0578-0.02980.31520.0326-0.4048-0.0170.1748-0.0273-0.00670.33610.01580.2194-30.15122.344.737
22.6656-1.866-0.2813.3910.33332.69570.15820.06430.2141-0.1246-0.0494-0.3491-0.02350.2766-0.09530.2284-0.0609-0.0160.3326-0.00510.2365-2.48658.425144.0471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 158 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 158 )

+
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