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- PDB-3mgq: Binding of Nickel ions to the Nucleosome Core Particle -

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Basic information

Entry
Database: PDB / ID: 3mgq
TitleBinding of Nickel ions to the Nucleosome Core Particle
Components
  • (DNA (147-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / 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 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 H2A / Histone 2A / 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 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / 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: 2.65 Å
AuthorsMohideen, K. / Muhammad, R. / Davey, C.A.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Perturbations in nucleosome structure from heavy metal association.
Authors: Mohideen, K. / Muhammad, R. / Davey, C.A.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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_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.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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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 (147-MER)
J: DNA (147-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,34061
Polymers197,44010
Non-polymers2,90051
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58740 Å2
ΔGint-363 kcal/mol
Surface area73220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.129, 109.643, 183.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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) / Gene: Histone 3 or H3 / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / 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) / Gene: Histone 4 or H4 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 12941.095 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: Histone 2A or H2A, LOC494591 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / 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) / Gene: Histone 2B or H2B / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (147-MER)


Mass: 45368.051 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic Palindromic DNA expressed in pUC18 plasmid using E.coli HB101 cells.
#6: DNA chain DNA (147-MER)


Mass: 45359.035 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic Palindromic DNA expressed in pUC18 plasmid using E.coli HB101 cells.

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Non-polymers , 2 types, 51 molecules

#7: Chemical...
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: Ni
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

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Details

Sequence detailsTHE CONFLICTS REPRESENT UNINTENTIONAL MUTATION OR VARIATION 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.48 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2009 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 2.65→94.07 Å / Num. all: 61576 / Num. obs: 60265 / % possible obs: 98.2 % / Redundancy: 5.6 % / Biso Wilson estimate: 79.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.7
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2 / Num. unique all: 7953 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMACRigid Bodyrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACRigid Bodyphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KX5

1kx5


Resolution: 2.65→51 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.065 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.649 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27613 1248 2 %RANDOM
Rwork0.23229 ---
obs0.23319 60265 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2---3.41 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.65→51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6169 6021 51 0 12241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02113004
X-RAY DIFFRACTIONr_angle_refined_deg1.4982.54418813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1585766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25521.131274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.104151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1061589
X-RAY DIFFRACTIONr_chiral_restr0.0780.22135
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027664
X-RAY DIFFRACTIONr_nbd_refined0.2130.25102
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2343
X-RAY DIFFRACTIONr_metal_ion_refined0.1480.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.22
X-RAY DIFFRACTIONr_mcbond_it0.8141.53930
X-RAY DIFFRACTIONr_mcangle_it1.4726183
X-RAY DIFFRACTIONr_scbond_it1.265312247
X-RAY DIFFRACTIONr_scangle_it2.254.512630
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 76 -
Rwork0.339 3693 -
obs--82.27 %

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