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- PDB-1k5j: The Crystal Structure of Nucleoplasmin-Core -

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Basic information

Entry
Database: PDB / ID: 1k5j
TitleThe Crystal Structure of Nucleoplasmin-Core
ComponentsNucleoplasmin Core
KeywordsCHAPERONE / beta-barrel / jellyroll / beta-bulge / pentamer
Function / homology
Function and homology information


sperm DNA decondensation / importin-alpha family protein binding / histone chaperone activity / nucleosome binding / positive regulation of DNA replication / histone binding / chromatin remodeling / chromatin binding / nucleolus / RNA binding ...sperm DNA decondensation / importin-alpha family protein binding / histone chaperone activity / nucleosome binding / positive regulation of DNA replication / histone binding / chromatin remodeling / chromatin binding / nucleolus / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
Nucleoplasmin core domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDutta, S. / Akey, I.V. / Dingwall, C. / Hartman, K.L. / Laue, T. / Nolte, R.T. / Head, J.F. / Akey, C.W.
CitationJournal: Mol.Cell / Year: 2001
Title: The crystal structure of nucleoplasmin-core: implications for histone binding and nucleosome assembly.
Authors: Dutta, S. / Akey, I.V. / Dingwall, C. / Hartman, K.L. / Laue, T. / Nolte, R.T. / Head, J.F. / Akey, C.W.
History
DepositionOct 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoplasmin Core
B: Nucleoplasmin Core
C: Nucleoplasmin Core
D: Nucleoplasmin Core
E: Nucleoplasmin Core


Theoretical massNumber of molelcules
Total (without water)68,7635
Polymers68,7635
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-86 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.700, 67.100, 101.700
Angle α, β, γ (deg.)90.00, 123.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nucleoplasmin Core


Mass: 13752.683 Da / Num. of mol.: 5 / Fragment: Nucleoplasmin core / Mutation: D27N, N61H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Nucleoplasmin / Plasmid: pRK172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05221
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, magnesium chloride, PEG-400, 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
20.1 MHEPES1reservoir
30.2 M1reservoirMgCl2
45 %PEG4001reservoir
522-27 %2-propanol1reservoir
620 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Jan 18, 1998
RadiationMonochromator: Double Crystal SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→90 Å / Num. all: 33535 / Num. obs: 30584 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 19
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 4 / % possible all: 94.8
Reflection
*PLUS
Num. measured all: 250956
Reflection shell
*PLUS
Mean I/σ(I) obs: 4.05

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2516 1373 random
Rwork0.2189 --
all0.251 29400 -
obs0.251 27856 -
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 0 147 3627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.286 217 -
Rwork0.262 --
obs-4103 89.1 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / σ(F): 0 / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.38
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / Rfactor Rwork: 0.262

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