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- PDB-3lz0: Crystal Structure of Nucleosome Core Particle Composed of the Wid... -

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Basic information

Entry
Database: PDB / ID: 3lz0
TitleCrystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1)
Components
  • (DNA (145-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / nucleosome / 601-sequence DNA / NCP and Nucleosome core / 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 H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVasudevan, D. / Chua, E.Y.D. / Davey, C.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structures of nucleosome core particles containing the '601' strong positioning sequence
Authors: Vasudevan, D. / Chua, E.Y. / Davey, C.A.
History
DepositionMar 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 14, 2012Group: Database references / Structure summary
Revision 1.3Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (145-MER)
J: DNA (145-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,73520
Polymers196,22510
Non-polymers51010
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56810 Å2
ΔGint-373 kcal/mol
Surface area71170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.370, 109.660, 175.750
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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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: P84233
#2: 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) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 12941.095 Da / Num. of mol.: 2 / Fragment: residues 2-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / 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) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(pLysS) / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#6: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct

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Non-polymers , 2 types, 10 molecules

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


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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Details

Sequence detailsUNINTENTIONAL MUTATIONS OR VARIATIONS IN GENOMIC SOURCES.

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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: 2.64 Å3/Da / Density % sol: 53.35 % / Mosaicity: 0.5 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: K cacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→93.04 Å / Num. all: 65509 / Num. obs: 65509 / % possible obs: 90.6 % / Redundancy: 4.6 % / Rsym value: 0.08 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.642.10.3841.91357963620.38461.9
2.64-2.82.60.3082.42027178080.30879.4
2.8-2.993.40.262.82943986620.2693.2
2.99-3.235.30.2013.34555286330.20199.7
3.23-3.545.80.1354.44626480310.13599.9
3.54-3.955.60.1085.34054772780.10899.9
3.95-4.565.40.08173476964440.08199.8
4.56-5.595.90.0817.53256454970.08199.9
5.59-7.915.60.0619.12401943150.06199.9
7.91-107.374.90.0655.11204224790.06598.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NCP146b (pdb code 1KX4)

1kx4


Resolution: 2.5→93.04 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.431 / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.599 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1317 2 %RANDOM
Rwork0.268 ---
all0.268 ---
obs0.269 65180 89.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 222.72 Å2 / Biso mean: 109.277 Å2 / Biso min: 43.71 Å2
Baniso -1Baniso -2Baniso -3
1-7.93 Å20 Å20 Å2
2---7.46 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→93.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5959 5939 10 0 11908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02112700
X-RAY DIFFRACTIONr_angle_refined_deg1.4532.54818400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8355743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72121.353266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.849151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8381583
X-RAY DIFFRACTIONr_chiral_restr0.0830.22097
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027474
X-RAY DIFFRACTIONr_nbd_refined0.2240.25839
X-RAY DIFFRACTIONr_nbtor_refined0.310.27873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2477
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.370.23
X-RAY DIFFRACTIONr_mcbond_it0.6351.53795
X-RAY DIFFRACTIONr_mcangle_it1.13925995
X-RAY DIFFRACTIONr_scbond_it0.901312085
X-RAY DIFFRACTIONr_scangle_it1.6344.512405
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.53 63 -
Rwork0.46 2789 -
all-2852 -
obs--53.79 %

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