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- PDB-6jqv: Crystal structure of Arabidopsis thaliana NRP2 -

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Basic information

Entry
Database: PDB / ID: 6jqv
TitleCrystal structure of Arabidopsis thaliana NRP2
ComponentsNAP1-related protein 2
KeywordsCHAPERONE / Nucleosome assembly protein NRP2 NAP NRP
Function / homology
Function and homology information


somatic cell DNA recombination / double-strand break repair via homologous recombination / nucleosome assembly / histone binding / chromatin binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nucleosome assembly protein / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Arylsulfatase, C-terminal domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NAP1-related protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsKumar, A. / Vasudevan, D.
CitationJournal: Molecules / Year: 2019
Title: Structural Characterization ofArabidopsis thalianaNAP1-Related Protein 2 (AtNRP2) and Comparison with its Homolog AtNRP1.
Authors: Kumar, A. / Kumar Singh, A. / Chandrakant Bobde, R. / Vasudevan, D.
History
DepositionApr 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: 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: NAP1-related protein 2
B: NAP1-related protein 2


Theoretical massNumber of molelcules
Total (without water)49,4172
Polymers49,4172
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-28 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.450, 123.450, 228.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein NAP1-related protein 2 / Nucleosome/chromatin assembly factor group A5 / Protein SET homolog 2


Mass: 24708.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NRP2, NFA5, At1g18800, F6A14.10 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8LC68

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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: 3.44 Å3/Da / Density % sol: 64.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M potassium fluoride, 2.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.42→42.04 Å / Num. obs: 9304 / % possible obs: 99.69 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1281 / Rpim(I) all: 0.03955 / Rrim(I) all: 0.1342 / Net I/σ(I): 17.37
Reflection shellResolution: 3.422→3.544 Å / Redundancy: 12 % / Mean I/σ(I) obs: 2.31 / Num. unique obs: 914 / CC1/2: 0.722 / Rpim(I) all: 0.3697 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DAY

5day


Resolution: 3.42→42.04 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.1
RfactorNum. reflection% reflection
Rfree0.3202 461 4.96 %
Rwork0.2722 --
obs0.2746 9286 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.42→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 0 0 2347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032394
X-RAY DIFFRACTIONf_angle_d0.6153252
X-RAY DIFFRACTIONf_dihedral_angle_d2.6291424
X-RAY DIFFRACTIONf_chiral_restr0.041372
X-RAY DIFFRACTIONf_plane_restr0.005415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4199-3.91470.38041600.29952867X-RAY DIFFRACTION99
3.9147-4.93150.34881430.26312932X-RAY DIFFRACTION100
4.9315-52.05860.28811580.26953026X-RAY DIFFRACTION99

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