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- PDB-3ut9: Crystal Structure of Nucleosome Core Particle Assembled with a Pa... -

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Basic information

Entry
Database: PDB / ID: 3ut9
TitleCrystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L)
Components
  • (145-mer DNA) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / Nucleosome core particle / NCP / 601-sequence DNA / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChua, E.Y.D. / Vasudevan, D. / Davey, G.E. / Wu, B. / Davey, C.A.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The mechanics behind DNA sequence-dependent properties of the nucleosome
Authors: Chua, E.Y.D. / Vasudevan, D. / Davey, G.E. / Wu, B. / Davey, C.A.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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.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_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: 145-mer DNA
J: 145-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,04343
Polymers198,30110
Non-polymers1,74233
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62460 Å2
ΔGint-531 kcal/mol
Surface area71690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.494, 109.533, 174.822
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(DE3)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(DE3)pLysS / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#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(DE3)pLysS / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain 145-mer DNA


Mass: 44761.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct
#6: DNA chain 145-mer DNA


Mass: 44752.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic construct

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Non-polymers , 4 types, 173 molecules

#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Mn
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.16 % / Mosaicity: 0.3 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.2→92.819 Å / Num. all: 104105 / Num. obs: 104105 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rsym value: 0.054 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.323.40.7340.5071.550703149360.3820.7340.5071.699
2.32-2.465.20.4840.3891.973457142200.210.4840.3892.999.9
2.46-2.636.10.3250.2732.681657134400.1310.3250.2734.5100
2.63-2.845.70.190.1574.371293125090.0790.190.1576.8100
2.84-3.115.90.1140.0956.368726115590.0470.1140.09510.9100
3.11-3.485.70.0750.0638.559788104890.0310.0750.06317.3100
3.48-4.025.90.0570.04810.95447292900.0230.0570.04824.4100
4.02-4.925.70.0520.04412.44516679020.0220.0520.04428.8100
4.92-6.965.90.050.04213.73636462070.0210.050.04230.6100
6.96-42.5455.30.0580.0476.91868535530.0270.0580.04732.299.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.3263 / WRfactor Rwork: 0.2782 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7123 / SU B: 9.836 / SU ML: 0.244 / SU R Cruickshank DPI: 0.272 / SU Rfree: 0.2216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 2083 2 %RANDOM
Rwork0.2565 ---
obs0.2572 104004 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 199.99 Å2 / Biso mean: 87.9913 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1-5.37 Å20 Å20 Å2
2---4.73 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6068 5939 33 140 12180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02112811
X-RAY DIFFRACTIONr_angle_refined_deg1.3622.54318543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41121.131274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.952151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3611589
X-RAY DIFFRACTIONr_chiral_restr0.0740.22108
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027558
X-RAY DIFFRACTIONr_nbd_refined0.2040.24701
X-RAY DIFFRACTIONr_nbtor_refined0.3040.27929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2432
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.22
X-RAY DIFFRACTIONr_mcbond_it0.7951.53782
X-RAY DIFFRACTIONr_mcangle_it1.41626085
X-RAY DIFFRACTIONr_scbond_it1.25639494
X-RAY DIFFRACTIONr_scangle_it1.8864.512458
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 140 -
Rwork0.357 7351 -
all-7491 -
obs--98.22 %

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