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- PDB-5t5k: Structure of histone-based chromatin in Archaea -

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Basic information

Entry
Database: PDB / ID: 5t5k
TitleStructure of histone-based chromatin in Archaea
Components
  • (DNA (90-MER)) x 2
  • DNA-binding protein HMf-2
KeywordsDNA BINDING PROTEIN/DNA / Nucleosome / Chromatin / Archaea Histones / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA topological change / protein homooligomerization / chromosome / double-stranded DNA binding / protein heterodimerization activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Histone, subunit A / Histone, subunit A / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / DNA / DNA (> 10) / DNA-binding protein HMf-2
Similarity search - Component
Biological speciesMethanothermus fervidus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBhattacharyya, S. / Mattiroli, F. / Dyer, P.N. / Sandman, K. / Reeve, J.N. / Luger, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 067777 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM53185 United States
CitationJournal: Science / Year: 2017
Title: Structure of histone-based chromatin in Archaea.
Authors: Mattiroli, F. / Bhattacharyya, S. / Dyer, P.N. / White, A.E. / Sandman, K. / Burkhart, B.W. / Byrne, K.R. / Lee, T. / Ahn, N.G. / Santangelo, T.J. / Reeve, J.N. / Luger, K.
History
DepositionAug 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein HMf-2
B: DNA-binding protein HMf-2
C: DNA-binding protein HMf-2
D: DNA-binding protein HMf-2
E: DNA-binding protein HMf-2
F: DNA-binding protein HMf-2
I: DNA (90-MER)
J: DNA (90-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,02611
Polymers101,6158
Non-polymers4113
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27420 Å2
ΔGint-198 kcal/mol
Surface area46790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.454, 99.454, 171.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
DNA-binding protein HMf-2 / Archaeal histone B


Mass: 7683.054 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus (archaea) / Gene: hmfB / Production host: Escherichia coli (E. coli) / References: UniProt: P19267
#2: DNA chain DNA (90-MER)


Mass: 27688.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (90-MER)


Mass: 27827.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2

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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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM MgAc, 50 mM Na Cacodylate pH 6.5, 10% PEG 400 under silicon oil
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4→19.76 Å / Num. obs: 8122 / % possible obs: 99.2 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 19.9
Reflection shellResolution: 4→4.22 Å / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 5.7 / Num. measured obs: 1183 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A7W

1a7w


Resolution: 4→19.76 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.25
RfactorNum. reflection% reflection
Rfree0.2618 373 4.62 %
Rwork0.2144 --
obs0.2165 8070 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 3690 15 0 6831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037294
X-RAY DIFFRACTIONf_angle_d0.53710598
X-RAY DIFFRACTIONf_dihedral_angle_d27.1423058
X-RAY DIFFRACTIONf_chiral_restr0.0191214
X-RAY DIFFRACTIONf_plane_restr0.002722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.57270.27531150.25452568X-RAY DIFFRACTION100
4.5727-5.73760.25651340.23212554X-RAY DIFFRACTION100
5.7376-19.75970.25771240.17952575X-RAY DIFFRACTION99
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)
17.4253-5.62193.06327.1681-2.98693.58870.083-0.46150.0852-0.91140.3702-0.0885-0.22290.2689-0.3270.5439-0.1411-0.00210.2463-0.09610.4145108.294515.7373.8653
25.3342-5.1787-2.59239.11323.51345.5801-0.0371-0.3013-0.40850.6325-0.51740.5580.385-0.89610.46390.1846-0.0326-0.04230.5816-0.01310.499683.8021-6.2457-5.9447
37.2982-2.35713.58982.2053-1.19563.86750.52210.81150.0607-0.2484-0.25050.0929-0.41120.2136-0.17330.5521-0.12760.05850.2574-0.11890.6193103.698717.38820.5122
43.9835-1.2992-0.22.979-2.05624.73790.0462-0.08310.491-0.48720.4278-0.9953-0.10320.7491-0.29630.26220.01860.06210.56420.01610.5442117.5203-0.1933-19.1421
52.02983.4193-1.64036.2947-3.17034.01590.0608-0.60650.64320.2530.08840.4045-0.05090.405-0.1120.23660.18440.00490.5601-0.07450.7388116.7871-4.8787-15.8661
65.4644-5.1168-4.74174.82244.2647.39740.23670.8288-0.5692-0.1571-0.4440.16390.7047-0.88120.16480.491-0.12870.00170.33130.00850.651586.0304-10.5303-9.3718
71.8965-0.3413-0.72092.01950.40192.76790.0448-0.08090.1281-0.07650.0173-0.1065-0.2030.1362-0.05870.5645-0.0442-0.21830.63020.15170.7081104.25444.2448-8.6541
82.1381-0.5127-0.68132.56950.91093.11230.16940.09070.14210.17950.0061-0.2371-0.14780.1665-0.12080.6395-0.0035-0.02020.54490.22640.3914104.97743.2716-7.5948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:67 )A1 - 67
2X-RAY DIFFRACTION2( CHAIN C AND RESID 1:68 )C1 - 68
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:68 )B1 - 68
4X-RAY DIFFRACTION4( CHAIN E AND RESID 1:67 )E1 - 67
5X-RAY DIFFRACTION5( CHAIN F AND RESID 1:67 )F1 - 67
6X-RAY DIFFRACTION6( CHAIN D AND RESID 1:67 )D1 - 67
7X-RAY DIFFRACTION7( CHAIN I AND RESID 1:90 )I1 - 90
8X-RAY DIFFRACTION8( CHAIN J AND RESID 1:90 )J1 - 90

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