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- PDB-6o6k: HUaa 19bp SYM DNA pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 6o6k
TitleHUaa 19bp SYM DNA pH 5.5
Components
  • DNA (5'-D(P*AP*TP*TP*TP*CP*AP*TP*GP*AP*T)-3')
  • DNA (5'-D(P*CP*AP*TP*CP*AP*TP*GP*AP*AP*A)-3')
  • DNA-binding protein HU-alpha
Keywordsdna binding protein/dna / Nucleoid Associated Protein / DNA supercoiling / Histone like proteins / DNA BINDING PROTEIN / dna binding protein-dna complex
Function / homology
Function and homology information


HU-DNA complex / bacterial nucleoid DNA packaging / DnaA-HU complex / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA damage response / DNA-templated transcription / DNA binding ...HU-DNA complex / bacterial nucleoid DNA packaging / DnaA-HU complex / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA damage response / DNA-templated transcription / DNA binding / membrane / identical protein binding / cytosol
Similarity search - Function
HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA-binding protein HU-alpha / DNA-binding protein HU-alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.601 Å
AuthorsRemesh, S.G. / Hammel, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)Integrated Diffraction Analysis Technologies United States
CitationJournal: Nat Commun / Year: 2020
Title: Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.
Authors: Remesh, S.G. / Verma, S.C. / Chen, J.H. / Ekman, A.A. / Larabell, C.A. / Adhya, S. / Hammel, M.
History
DepositionMar 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 HU-alpha
B: DNA-binding protein HU-alpha
C: DNA (5'-D(P*AP*TP*TP*TP*CP*AP*TP*GP*AP*T)-3')
D: DNA (5'-D(P*CP*AP*TP*CP*AP*TP*GP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)25,1714
Polymers25,1714
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-48 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.790, 84.790, 63.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein DNA-binding protein HU-alpha / HU-2 / NS2


Mass: 9549.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hupA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0ACF2, UniProt: P0ACF0*PLUS
#2: DNA chain DNA (5'-D(P*AP*TP*TP*TP*CP*AP*TP*GP*AP*T)-3')


Mass: 3034.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*CP*AP*TP*CP*AP*TP*GP*AP*AP*A)-3')


Mass: 3037.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.02M ZnCl2, 20% PEG 3350 / PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.994→84.789 Å / Num. all: 71317 / Num. obs: 2939 / % possible obs: 99.7 % / Redundancy: 13.8 % / CC1/2: 1 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.141 / Net I/σ(I): 15.1
Reflection shellResolution: 3.602→3.73 Å / Redundancy: 12.9 % / Num. unique obs: 18426 / CC1/2: 0.245 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YEX and DNA

4yex


Resolution: 3.601→59.956 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.74
RfactorNum. reflection% reflection
Rfree0.3019 294 10.01 %
Rwork0.2523 --
obs0.2571 2937 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.601→59.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 409 0 0 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031544
X-RAY DIFFRACTIONf_angle_d0.5252158
X-RAY DIFFRACTIONf_dihedral_angle_d25.279592
X-RAY DIFFRACTIONf_chiral_restr0.034262
X-RAY DIFFRACTIONf_plane_restr0.002203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6007-4.53620.38111420.28741279X-RAY DIFFRACTION100
4.5362-59.96390.26771520.23761365X-RAY DIFFRACTION100
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)
10.2949-0.192-0.02920.0119-0.17020.04711.00910.09110.09062.3441-0.44031.03640.5492-0.142601.0895-0.2490.2860.73250.03680.6975-6.660516.6635.33
20.9354-0.3580.8265-0.0521-0.41-0.04741.6490.37096.03520.8854-1.7714-2.25840.0059-1.1273-00.26660.19320.02611.02960.24251.48641.85228.016526.5261
30.04570.0264-0.0424-0.14240.0480.008-0.94360.20680.5359-0.6501-1.8635-2.5846-0.32960.021-01.44750.5705-0.07012.05250.53841.71485.596830.41631.5591
40.13430.0194-0.04280.04880.24870.22490.13341.5462-1.038-1.6748-0.07881.49790.6065-0.468200.71240.16680.00171.36320.35450.86858.526915.627120.0921
5-0.0153-0.0561-0.1771-0.04730.0175-0.1027-0.45980.53941.4613-0.1008-2.34230.4821-1.11022.043901.0218-0.05450.0791.5426-0.44322.15064.229431.275535.5019
60.60520.3623-0.67060.4133-0.65490.2762-0.4261-0.271-0.10040.504-0.25840.64690.9385-0.445800.6269-0.0778-0.05550.6334-0.01680.60420.529916.593930.9966
7-0.4206-0.0060.50640.04790.1178-0.2133-1.98093.7257-0.3922-0.54881.15363.83130.5675-0.4837-00.6006-0.2115-0.28351.32370.45010.5926-1.874420.589417.0265
80.2330.01210.87590.0252-0.29060.27410.87480.39520.2033-0.338-0.31110.3155-0.28640.2457-01.4921-0.0693-0.21191.52750.2471.4811-21.034722.914817.7641
9-0.5571-0.02720.21720.03020.4226-0.00910.5155-0.1020.25870.29780.0744-0.5728-0.3633-1.453701.0728-0.11110.05721.33730.2371.0022-19.953522.020314.6198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:17 )A1 - 17
2X-RAY DIFFRACTION2( CHAIN A AND RESID 18:53 )A18 - 53
3X-RAY DIFFRACTION3( CHAIN A AND RESID 54:75 )A54 - 75
4X-RAY DIFFRACTION4( CHAIN A AND RESID 76:90 )A76 - 90
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:17 )B1 - 17
6X-RAY DIFFRACTION6( CHAIN B AND RESID 18:44 )B18 - 44
7X-RAY DIFFRACTION7( CHAIN B AND RESID 45:89 )B45 - 89
8X-RAY DIFFRACTION8( CHAIN C AND RESID 5:10 )C5 - 10
9X-RAY DIFFRACTION9( CHAIN D AND RESID 1:10 )D1 - 10

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