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- PDB-2nzd: Nucleosome core particle containing 145 bp of DNA -

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Basic information

Entry
Database: PDB / ID: 2nzd
TitleNucleosome core particle containing 145 bp of DNA
Components
  • (DNA (145-MER)) x 2
  • Histone H2B
  • Histone H3
  • Histone H4
  • histone H2A
KeywordsSTRUCTURAL PROTEIN/DNA / nucleosome / chromatin / histone / DNA stretching / DNA kinking / double-helix / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsOng, M.S. / Richmond, T.J. / Davey, C.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: DNA stretching and extreme kinking in the nucleosome core
Authors: Ong, M.S. / Richmond, T.J. / Davey, C.A.
History
DepositionNov 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DNA (145-MER)
J: DNA (145-MER)
A: Histone H3
B: Histone H4
C: histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: histone H2A
H: Histone H2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,80721
Polymers196,20310
Non-polymers60411
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.617, 109.856, 181.217
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules IJ

#1: DNA chain DNA (145-MER)


Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (145-MER)


Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 4 types, 8 molecules AEBFCGDH

#3: Protein Histone H3


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: GenBank: 288992, UniProt: P84233*PLUS
#4: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#5: Protein histone H2A


Mass: 12941.095 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#6: Protein Histone H2B / H2B1.1


Mass: 13848.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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Non-polymers , 2 types, 133 molecules

#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MnCl211
2KCl11
3K-Cacodylate11
4HOH11
5MnCl212
6KCl12
7K-Cacodylate12
8HOH12

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 5, 2006 / Details: osmic mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.65→50.7 Å / Num. all: 61751 / Num. obs: 56193 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 20.9
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / Num. measured all: 27467 / Num. unique all: 5579 / Rsym value: 0.48 / % possible all: 63.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1KX3

1kx3


Resolution: 2.65→40 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.836 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.887 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1136 2 %RANDOM
Rwork0.233 ---
all0.234 61932 --
obs0.234 56123 90.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.218 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2---1.09 Å20 Å2
3----0.78 Å2
Refine analyzeLuzzati coordinate error free: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 5939 11 122 12158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02112821
X-RAY DIFFRACTIONr_angle_refined_deg1.452.54318556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0865757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50921.338269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.427151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4371584
X-RAY DIFFRACTIONr_chiral_restr0.0740.22113
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027545
X-RAY DIFFRACTIONr_nbd_refined0.2060.24850
X-RAY DIFFRACTIONr_nbtor_refined0.3090.27995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2396
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.25
X-RAY DIFFRACTIONr_mcbond_it0.7271.53872
X-RAY DIFFRACTIONr_mcangle_it1.29226110
X-RAY DIFFRACTIONr_scbond_it1.234312076
X-RAY DIFFRACTIONr_scangle_it2.2024.512446
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 59 -
Rwork0.302 2573 -
obs-2632 58.46 %

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