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- PDB-6a6y: Crystal Structure of Asf1 from Plasmodium falciparum -

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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


DNA replication-dependent chromatin assembly / nucleosome disassembly / unfolded protein binding / nucleosome assembly / histone binding / chromatin binding / chromatin / nucleus
Similarity search - Function
Histone chaperone ASF1-like / Histone deposition protein Asf1 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


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


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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 )

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