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- PDB-3gyw: Crystal structure of nucleosome assembly protein from Plasmodium ... -

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Basic information

Entry
Database: PDB / ID: 3gyw
TitleCrystal structure of nucleosome assembly protein from Plasmodium falciparum at 2.4 A resolution
ComponentsNucleosome assembly protein 1, putative
KeywordsCHAPERONE / SIR / SIRAS / NUCLEOSOME ASSEMBLY PROTEIN / HISTONE RECOGNITION
Function / homology
Function and homology information


nucleosome assembly / histone binding / chromatin binding / protein kinase binding / chromatin / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1500 / Nucleosome assembly protein / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Arylsulfatase, C-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Nucleosome assembly protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.4 Å
AuthorsYogavel, M. / Gill, J. / Sharma, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Iodide-SAD, SIR and SIRAS phasing for structure solution of a nucleosome assembly protein.
Authors: Yogavel, M. / Gill, J. / Sharma, A.
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Nucleosome assembly protein 1, putative


Theoretical massNumber of molelcules
Total (without water)29,6681
Polymers29,6681
Non-polymers00
Water77543
1
A: Nucleosome assembly protein 1, putative

A: Nucleosome assembly protein 1, putative


Theoretical massNumber of molelcules
Total (without water)59,3352
Polymers59,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4140 Å2
ΔGint-32 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.24, 37.87, 79.14
Angle α, β, γ (deg.)90.00, 99.7, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleosome assembly protein 1, putative


Mass: 29667.742 Da / Num. of mol.: 1 / Fragment: residues 33-281 (UNP residues 45-293)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: pfl0185c / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8I608
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 20% PEG 3350, 0.2M magnesium chloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 8943 / Num. obs: 8943 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 37.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 8.1 / Num. unique all: 892 / % possible all: 100

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Processing

Software
NameClassification
MAR345dtbdata collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 889 -RANDOM
Rwork0.22 ---
all0.224 8942 --
obs-8942 99.96 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 0 43 1584
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.007
X-RAY DIFFRACTIONr_angle_refined_deg0.981
LS refinement shellResolution: 2.4→2.462 Å
RfactorNum. reflection% reflection
Rfree0.267 53 -
Rwork0.25 --
obs-594 99.7 %

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