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- PDB-4yew: HUab-19bp -

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Basic information

Entry
Database: PDB / ID: 4yew
TitleHUab-19bp
Components
  • (synthetic DNA strand) x 2
  • DNA-binding protein HU-alpha
  • DNA-binding protein HU-beta
KeywordsDNA BINDING PROTEIN/DNA / HU-DNA / transcription / pathogenicity / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


HU-DNA complex / DnaA-HU complex / bacterial nucleoid DNA packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA damage response / DNA binding ...HU-DNA complex / DnaA-HU complex / bacterial nucleoid DNA packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA damage response / DNA binding / identical protein binding / membrane / 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 (> 10) / : / DNA-binding protein HU-alpha / DNA-binding protein HU-alpha / DNA-binding protein HU-beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.683 Å
AuthorsHammel, M. / Reyes, F.E. / Parpana, R. / Tainer, J.A. / Adhya, S. / Amlanjyoti, D.
CitationJournal: Sci Adv / Year: 2016
Title: HU multimerization shift controls nucleoid compaction.
Authors: Hammel, M. / Amlanjyoti, D. / Reyes, F.E. / Chen, J.H. / Parpana, R. / Tang, H.Y. / Larabell, C.A. / Tainer, J.A. / Adhya, S.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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

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Assembly

Deposited unit
A: DNA-binding protein HU-beta
B: synthetic DNA strand
D: synthetic DNA strand
C: DNA-binding protein HU-alpha


Theoretical massNumber of molelcules
Total (without water)24,6214
Polymers24,6214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.460, 84.460, 63.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein DNA-binding protein HU-beta


Mass: 9169.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupB, hopD, b0440, JW0430 / Production host: Escherichia coli (E. coli) / References: UniProt: N4NVB4, UniProt: P0ACF4*PLUS
#2: DNA chain synthetic DNA strand


Mass: 2605.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain synthetic DNA strand


Mass: 3296.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Protein DNA-binding protein HU-alpha / HU-2 / NS2


Mass: 9549.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupA, b4000, JW3964 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACF2, UniProt: P0ACF0*PLUS
Sequence detailsDNA sample sequence used in experiment is 5'-TTCAATTGTTGTTAACTTG-3'. But the asymmetric unit ...DNA sample sequence used in experiment is 5'-TTCAATTGTTGTTAACTTG-3'. But the asymmetric unit contains multiple, out-of-register duplex positions, so the DNA chain is modeled according to averaged density.

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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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 30% PEG MME 550, 0.05 M CaCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2013 / Details: Q315R
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.683→84.461 Å / Num. all: 6882 / Num. obs: 6882 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.4 / Num. measured all: 56788
Reflection shellResolution: 2.683→2.692 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.58 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
Aimlessdata scaling
BUSTER2.10.0refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUL

1mul


Resolution: 2.683→59.72 Å / Cor.coef. Fo:Fc: 0.9208 / Cor.coef. Fo:Fc free: 0.8915 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.753 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.94 / SU Rfree Blow DPI: 0.361 / SU Rfree Cruickshank DPI: 0.354
Details: The asymmetric unit of the crystal contains multiple, out-of-register duplex positions, such that backbones superimpose, but base identity differs. The density is an average of all ...Details: The asymmetric unit of the crystal contains multiple, out-of-register duplex positions, such that backbones superimpose, but base identity differs. The density is an average of all nucleotides, and the DNA chain was built accordingly.
RfactorNum. reflection% reflectionSelection details
Rfree0.2903 326 4.76 %RANDOM
Rwork0.2497 ---
obs0.2515 6853 99.3 %-
Displacement parametersBiso max: 160.91 Å2 / Biso mean: 76.558 Å2 / Biso min: 44.48 Å2
Baniso -1Baniso -2Baniso -3
1--4.6068 Å20 Å20 Å2
2---4.6068 Å20 Å2
3---9.2137 Å2
Refine analyzeLuzzati coordinate error obs: 0.494 Å
Refinement stepCycle: LAST / Resolution: 2.683→59.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 397 0 0 1433
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d474SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes26HARMONIC2
X-RAY DIFFRACTIONt_gen_planes168HARMONIC5
X-RAY DIFFRACTIONt_it1484HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion207SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1614SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1484HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2068HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion2.26
X-RAY DIFFRACTIONt_other_torsion22.31
LS refinement shellResolution: 2.683→3 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3108 83 4.42 %
Rwork0.3098 1794 -
all0.3099 1877 -
obs--99.3 %

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