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- PDB-2aro: Crystal Structure Of The Native Histone Octamer To 2.1 Angstrom R... -

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Basic information

Entry
Database: PDB / ID: 2aro
TitleCrystal Structure Of The Native Histone Octamer To 2.1 Angstrom Resolution, Crystalised In The Presence Of S-Nitrosoglutathione
Components
  • HISTONE H3
  • HISTONE H4-VI
  • Histone H2A-IV
  • Histone H2B
KeywordsSTRUCTURAL PROTEIN / OCTAMER / OXIDATION / ALLOSTERY / CIRCULAR DICHROISM
Function / homology
Function and homology information


PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Metalloprotease DUBs / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks ...PKMTs methylate histone lysines / HDMs demethylate histones / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Metalloprotease DUBs / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Interleukin-7 signaling / Chromatin modifying enzymes / HATs acetylate histones / Ub-specific processing proteases / PRC2 methylates histones and DNA / Oxidative Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / Deposition of new CENPA-containing nucleosomes at the centromere / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / structural constituent of chromatin / nucleosome / defense response to bacterium / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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
PHOSPHATE ION / Histone H2A-IV / Histone H2B 5 / Histone H2B 1/2/3/4/6 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWood, C.M. / Sodngam, S. / Nicholson, J.M. / Lambert, S.J. / Reynolds, C.D. / Baldwin, J.P.
CitationJournal: Biochim.Biophys.Acta / Year: 2006
Title: The oxidised histone octamer does not form a H3 disulphide bond.
Authors: Wood, C.M. / Sodngam, S. / Nicholson, J.M. / Lambert, S.J. / Reynolds, C.D. / Baldwin, J.P.
History
DepositionAug 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 H2A-IV
B: Histone H2B
C: HISTONE H3
D: HISTONE H4-VI
E: Histone H2A-IV
F: Histone H2B
G: HISTONE H3
H: HISTONE H4-VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,76736
Polymers109,4768
Non-polymers1,29028
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34300 Å2
ΔGint-476 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.084, 158.084, 101.037
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H2A-IV /


Mass: 13969.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02263
#2: Protein Histone H2B /


Mass: 13953.251 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02279, UniProt: P0C1H3*PLUS
#3: Protein HISTONE H3 /


Mass: 15421.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P84229
#4: Protein HISTONE H4-VI /


Mass: 11394.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P62801

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Non-polymers , 3 types, 486 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 71.37 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. obs: 81294

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TZY

1tzy


Resolution: 2.1→10 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.137 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.14
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22508 4070 5 %RANDOM
Rwork0.18381 ---
obs0.1859 77199 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5965 0 48 458 6471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226063
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9838154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32921.521263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.708151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9421580
X-RAY DIFFRACTIONr_chiral_restr0.1280.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024432
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.22842
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24167
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2402
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.251.53875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9326012
X-RAY DIFFRACTIONr_scbond_it3.21132449
X-RAY DIFFRACTIONr_scangle_it5.0934.52142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 287 -
Rwork0.245 5368 -
obs--96.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.73820.48730.40881.2210.79590.6376-0.07030.12350.053-0.20480.0981-0.0651-0.18610.0327-0.0278-0.038-0.02330.0247-0.18210.0045-0.1783-58.6546-14.3998-12.1309
20.62930.30590.48490.9520.34030.6125-0.0361-0.00530.0552-0.17840.0703-0.0491-0.09810.0274-0.0342-0.0506-0.00660.0312-0.192-0.0138-0.1471-53.9065-10.5551-5.7003
30.6054-0.0317-0.00060.70350.230.45260.0040.0164-0.0662-0.0398-0.0074-0.02540.05570.11380.0034-0.1620.03710.0134-0.1489-0.0268-0.1-41.0543-44.9285-3.4859
40.7292-0.2278-0.10821.02820.35710.49070.04460.03070.0289-0.0483-0.0314-0.0729-0.03310.1054-0.0132-0.16890.02710.0191-0.1376-0.0133-0.121-38.3553-36.5038-2.4474
50.478-0.4025-0.18820.79130.33380.6699-0.0277-0.1303-0.06620.06510.0232-0.01910.01650.03150.0046-0.13990.0003-0.0071-0.11510.0084-0.1647-54.159-37.928119.2252
60.835-0.39960.08980.95470.00090.6209-0.0077-0.13840.02650.03420.0292-0.0195-0.0765-0.0048-0.0216-0.1238-0.0010.0034-0.1142-0.0069-0.1847-58.4632-30.48321.4055
70.6527-0.00980.07850.2680.24130.6684-0.00160.0413-0.0871-0.0470.0537-0.0118-0.0332-0.0526-0.0521-0.13290.0035-0.0242-0.1427-0.0164-0.1461-72.8724-37.5852-12.4442
80.7642-0.0240.23770.49090.42930.79310.0149-0.0703-0.11330.01310.04-0.0046-0.0284-0.0965-0.0549-0.13040.0105-0.0062-0.13750.0213-0.1578-75.4618-33.6589-3.6258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 11814 - 119
2X-RAY DIFFRACTION2BB33 - 12434 - 125
3X-RAY DIFFRACTION3CC41 - 13542 - 136
4X-RAY DIFFRACTION4DD20 - 10221 - 103
5X-RAY DIFFRACTION5EE14 - 11715 - 118
6X-RAY DIFFRACTION6FF33 - 12534 - 126
7X-RAY DIFFRACTION7GG38 - 13539 - 136
8X-RAY DIFFRACTION8HH19 - 10220 - 103

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