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- PDB-1xb9: The structure and function of Xenopus NO38-core, a histone chaper... -

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Basic information

Entry
Database: PDB / ID: 1xb9
TitleThe structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus
ComponentsNucleophosminNPM1
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 / DNA repair / nucleolus / 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: 1.9 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
DepositionAug 30, 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

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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
Water5,495305
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 area9910 Å2
ΔGint-61 kcal/mol
Surface area21720 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 area9880 Å2
ΔGint-63 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.913, 64.549, 97.461
Angle α, β, γ (deg.)90.00, 113.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nucleophosmin / NPM1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, Tris-HCl, Calcium 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: Oct 30, 2002 / 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: 1.9→90 Å / Num. obs: 89372 / % possible obs: 94 % / Observed criterion σ(F): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.038 / Rsym value: 0.031 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.24 / Num. unique all: 369 / Rsym value: 0.19 / % possible all: 94

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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 1K5J

1k5j


Resolution: 1.9→91.29 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.036 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25504 6598 8.1 %RANDOM
Rwork0.20372 ---
obs0.20794 81414 91.1 %-
all-89377 --
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: 25.843 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-0.21 Å2
2---0.88 Å20 Å2
3---0.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8032 0 0 305 8337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0218175
X-RAY DIFFRACTIONr_bond_other_d0.0020.027521
X-RAY DIFFRACTIONr_angle_refined_deg2.5591.98611034
X-RAY DIFFRACTIONr_angle_other_deg1.119317666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.77951043
X-RAY DIFFRACTIONr_chiral_restr0.1830.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028983
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021453
X-RAY DIFFRACTIONr_nbd_refined0.2050.21221
X-RAY DIFFRACTIONr_nbd_other0.2730.28555
X-RAY DIFFRACTIONr_nbtor_other0.1030.25534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2326
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3210.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3160.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6560.215
X-RAY DIFFRACTIONr_mcbond_it1.5741.55249
X-RAY DIFFRACTIONr_mcangle_it2.40228426
X-RAY DIFFRACTIONr_scbond_it3.67332926
X-RAY DIFFRACTIONr_scangle_it5.3624.52608
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.262 488
Rwork0.211 5240
obs-5240

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