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- PDB-1xe0: The structure and function of Xenopus NO38-core, a histone bindin... -

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Basic information

Entry
Database: PDB / ID: 1xe0
TitleThe structure and function of Xenopus NO38-core, a histone binding chaperone in the nucleolus
ComponentsNucleophosmin
KeywordsCHAPERONE / NO38 / Drosophila Nucleoplasmin-Like Protein (dNLP) / Nucleoplasmin (Np) / histone binding
Function / homology
Function and homology information


regulation of endoribonuclease activity / regulation of endodeoxyribonuclease activity / regulation of centrosome duplication / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / histone binding / chromatin remodeling / ribonucleoprotein complex ...regulation of endoribonuclease activity / regulation of endodeoxyribonuclease activity / regulation of centrosome duplication / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / histone binding / chromatin remodeling / ribonucleoprotein complex / DNA repair / centrosome / chromatin binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Nucleoplasmin core domain / Nucleophosmin, C-terminal / Nucleophosmin C-terminal 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNamboodiri, V.M. / Akey, I.V. / Schmidt-Zachmann, M.S. / Head, J.F. / Akey, C.W.
CitationJournal: Structure / Year: 2004
Title: The Structure and Function of Xenopus NO38-Core, a Histone Chaperone in the Nucleolus.
Authors: Namboodiri, V.M. / Akey, I.V. / Schmidt-Zachmann, M.S. / Head, J.F. / Akey, C.W.
History
DepositionSep 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
A: Nucleophosmin
B: Nucleophosmin
C: Nucleophosmin
D: Nucleophosmin
E: Nucleophosmin
F: Nucleophosmin
G: Nucleophosmin
H: Nucleophosmin
I: Nucleophosmin
J: Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)123,52010
Polymers123,52010
Non-polymers00
Water6,575365
1
A: Nucleophosmin
B: Nucleophosmin
C: Nucleophosmin
D: Nucleophosmin
E: Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)61,7605
Polymers61,7605
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-57 kcal/mol
Surface area21270 Å2
MethodPISA
2
F: Nucleophosmin
G: Nucleophosmin
H: Nucleophosmin
I: Nucleophosmin
J: Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)61,7605
Polymers61,7605
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-59 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.0, 59.0, 87.2
Angle α, β, γ (deg.)77.0, 88.3, 60.9
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleophosmin / NPM / Nucleolar phosphoprotein B23 / Numatrin / Nucleolar protein NO38


Mass: 12351.986 Da / Num. of mol.: 10 / Fragment: N-terminal core (residues 16-124)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pPep-T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07222
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, Ethylene glycol, Tris-HCl, Magnesium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2004 / Details: Mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→90 Å / Num. obs: 109907 / % possible obs: 79.7 % / Observed criterion σ(F): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.03 / Rsym value: 0.031 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 4.2 / Num. unique all: 706 / Rsym value: 0.155 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XB9

1xb9


Resolution: 1.7→84.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.936 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25908 7879 8 %RANDOM
Rwork0.20834 ---
obs0.21239 90609 89.82 %-
all-98408 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.185 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0.78 Å20 Å2
2---0.03 Å20.83 Å2
3---0.11 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.7→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7963 0 0 365 8328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0218105
X-RAY DIFFRACTIONr_bond_other_d0.0020.027464
X-RAY DIFFRACTIONr_angle_refined_deg2.4391.98510933
X-RAY DIFFRACTIONr_angle_other_deg1.05317532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0851032
X-RAY DIFFRACTIONr_chiral_restr0.150.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.028894
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021442
X-RAY DIFFRACTIONr_nbd_refined0.2240.21169
X-RAY DIFFRACTIONr_nbd_other0.270.28518
X-RAY DIFFRACTIONr_nbtor_other0.0980.25423
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4540.2281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5330.211
X-RAY DIFFRACTIONr_mcbond_it1.3821.55199
X-RAY DIFFRACTIONr_mcangle_it2.15328340
X-RAY DIFFRACTIONr_scbond_it3.26332906
X-RAY DIFFRACTIONr_scangle_it4.9134.52593
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.315 563
Rwork0.25 6047
obs-6047

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