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- PDB-1hst: CRYSTAL STRUCTURE OF GLOBULAR DOMAIN OF HISTONE H5 AND ITS IMPLIC... -

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Basic information

Entry
Database: PDB / ID: 1hst
TitleCRYSTAL STRUCTURE OF GLOBULAR DOMAIN OF HISTONE H5 AND ITS IMPLICATIONS FOR NUCLEOSOME BINDING
ComponentsHISTONE H5Histone H1
KeywordsCHROMOSOMAL PROTEIN
Function / homology
Function and homology information


negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / double-stranded DNA binding / nucleus
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsRamakrishnan, V. / Finch, J.T. / Graziano, V. / Lee, P.L. / Sweet, R.M.
Citation
Journal: Nature / Year: 1993
Title: Crystal structure of globular domain of histone H5 and its implications for nucleosome binding.
Authors: Ramakrishnan, V. / Finch, J.T. / Graziano, V. / Lee, P.L. / Sweet, R.M.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization of the Globular Domain of Histone H5
Authors: Graziano, V. / Gerchman, S.E. / Wonacott, A.J. / Sweet, R.M. / Wells, J.R.E. / White, S.W. / Ramakrishnan, V.
History
DepositionMar 30, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTONE H5
B: HISTONE H5


Theoretical massNumber of molelcules
Total (without water)19,5792
Polymers19,5792
Non-polymers00
Water0
1
A: HISTONE H5


Theoretical massNumber of molelcules
Total (without water)9,7891
Polymers9,7891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HISTONE H5


Theoretical massNumber of molelcules
Total (without water)9,7891
Polymers9,7891
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.500, 80.400, 38.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: RESIDUES A 39 - A 44 AND B 39 - B 44 FORM A LOOP BETWEEN HELICES I AND II. THESE ARE NOT WELL DEFINED IN THE DENSITY, AND THEIR POSITIONS ARE ONLY PRELIMINARY.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7827, -0.2417, 0.5735), (0.2326, -0.9683, -0.0906), (0.5772, 0.0625, 0.8142)
Vector: 43.02, 34.07, -10.67)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. HOWEVER, THE CONFORMATION OF THE REGION FROM RESIDUE 78 TO RESIDUE 97 IS DIFFERENT IN THE TWO CHAINS.

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Components

#1: Protein HISTONE H5 / Histone H1


Mass: 9789.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell line: H5 / References: UniProt: P02259

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 212.253-257 1990
Components of the solutions
*PLUS
Conc.: 2.2 M / Common name: phosphate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→6 Å / Rfactor Rwork: 0.27 / Rfactor obs: 0.27 / σ(F): 0
Details: RESIDUES 24 - 96 ARE REPRESENTED IN THIS ENTRY, ALTHOUGH POORLY DEFINED DENSITY IS VISIBLE BEYOND RESIDUE 96 OF CHAIN *A*. OF THE 89 RESIDUES OF THE POLYPEPTIDE CHAIN, 5 RESIDUES AT THE N- ...Details: RESIDUES 24 - 96 ARE REPRESENTED IN THIS ENTRY, ALTHOUGH POORLY DEFINED DENSITY IS VISIBLE BEYOND RESIDUE 96 OF CHAIN *A*. OF THE 89 RESIDUES OF THE POLYPEPTIDE CHAIN, 5 RESIDUES AT THE N-TERMINUS AND 11 RESIDUES AT THE C-TERMINUS HAVE NOT BEEN INCLUDED IN THE MODEL; THUS THE R-FACTOR IS SOMEWHAT HIGH AT THIS POINT.
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 0 0 1128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 6 Å / σ(F): 0 / Rfactor all: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.1

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