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- PDB-3t30: Human nucleoplasmin (Npm2): a histone chaperone in oocytes and ea... -

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Basic information

Entry
Database: PDB / ID: 3t30
TitleHuman nucleoplasmin (Npm2): a histone chaperone in oocytes and early embryos
ComponentsNucleoplasmin-2
KeywordsCHAPERONE / beta-barrel jelly roll topology / Histone chaperone / H2A-H2B dimer and H3-H4 tetramer / oocytes and early embryos
Function / homology
Function and homology information


oocyte differentiation / positive regulation of meiotic nuclear division / regulation of exit from mitosis / blastocyst development / single fertilization / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of DNA replication / histone binding / chromatin remodeling / chromatin binding ...oocyte differentiation / positive regulation of meiotic nuclear division / regulation of exit from mitosis / blastocyst development / single fertilization / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of DNA replication / histone binding / chromatin remodeling / chromatin binding / chromatin / nucleolus / enzyme binding / RNA binding / nucleoplasm / identical protein binding / nucleus / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPlatonova, O. / Head, J.F. / Akey, C.W.
CitationJournal: Biochemistry / Year: 2011
Title: Crystal structure and function of human nucleoplasmin (npm2): a histone chaperone in oocytes and embryos.
Authors: Platonova, O. / Akey, I.V. / Head, J.F. / Akey, C.W.
History
DepositionJul 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nucleoplasmin-2
E: Nucleoplasmin-2
D: Nucleoplasmin-2
A: Nucleoplasmin-2
C: Nucleoplasmin-2
H: Nucleoplasmin-2
I: Nucleoplasmin-2
J: Nucleoplasmin-2
F: Nucleoplasmin-2
G: Nucleoplasmin-2


Theoretical massNumber of molelcules
Total (without water)123,94410
Polymers123,94410
Non-polymers00
Water12,106672
1
B: Nucleoplasmin-2
E: Nucleoplasmin-2
D: Nucleoplasmin-2
A: Nucleoplasmin-2
C: Nucleoplasmin-2


Theoretical massNumber of molelcules
Total (without water)61,9725
Polymers61,9725
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-79 kcal/mol
Surface area19820 Å2
MethodPISA
2
H: Nucleoplasmin-2
I: Nucleoplasmin-2
J: Nucleoplasmin-2
F: Nucleoplasmin-2
G: Nucleoplasmin-2


Theoretical massNumber of molelcules
Total (without water)61,9725
Polymers61,9725
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-81 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.03, 107.24, 108.7
Angle α, β, γ (deg.)90.00, 102.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoplasmin-2


Mass: 12394.425 Da / Num. of mol.: 10 / Fragment: NPM2 oligomerisation domain (UNP residues 14-122)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPM2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86SE8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% v/v PEG 3350, 100 mM NaCl, 25 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 76 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2007
RadiationMonochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→40.5 Å / Num. all: 86348 / Num. obs: 86130 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4 / Num. unique all: 8621 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1K5J (Xenopus nucleoplasmin)

1k5j


Resolution: 1.9→40.46 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1116 1.35 %random
Rwork0.1925 ---
all0.1932 82427 --
obs0.1932 82427 95.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.738 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.2854 Å20 Å26.0746 Å2
2---7.6396 Å2-0 Å2
3----8.6458 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7190 0 0 672 7862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177352
X-RAY DIFFRACTIONf_angle_d1.6599961
X-RAY DIFFRACTIONf_dihedral_angle_d17.8822768
X-RAY DIFFRACTIONf_chiral_restr0.1341170
X-RAY DIFFRACTIONf_plane_restr0.0091253
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9-1.98650.25061290.21649465958489
1.9865-2.09120.26151250.19719840996593
2.0912-2.22220.24121430.1841100021014594
2.2222-2.39380.23751400.1949101291026996
2.3938-2.63460.27011420.1972102671040997
2.6346-3.01580.28551420.2057104711061398
3.0158-3.79910.23881470.17871062010767100
3.7991-40.46910.21371480.1863105171066598

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