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- PDB-4p3v: Crystal structure of the E. coli HU beta2 protein -

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Basic information

Entry
Database: PDB / ID: 4p3v
TitleCrystal structure of the E. coli HU beta2 protein
ComponentsDNA-binding protein HU-beta
KeywordsDNA BINDING PROTEIN / Histone-like / homodimer
Function / homology
Function and homology information


HU-DNA complex / DnaA-HU complex / bacterial nucleoid packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA binding / 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-binding protein HU-beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsLe Meur, R. / Coste, F. / Castaing, B.
CitationJournal: To Be Published
Title: Crystal structure of the E. coli HU beta2 protein
Authors: Le meur, R. / Coste, F. / Castaing, B.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein HU-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2472
Polymers9,2401
Non-polymers71
Water2,036113
1
A: DNA-binding protein HU-beta
hetero molecules

A: DNA-binding protein HU-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4934
Polymers18,4792
Non-polymers142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area3920 Å2
ΔGint-45 kcal/mol
Surface area6940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.107, 51.107, 110.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-364-

HOH

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Components

#1: Protein DNA-binding protein HU-beta / HU-1 / NS1


Mass: 9239.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hupB, hopD, b0440, JW0430 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACF4
#2: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.31 Å3/Da / Density % sol: 47 % / Description: plate-like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG800, 0.2M lithium sulfate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98401 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98401 Å / Relative weight: 1
ReflectionResolution: 1.25→44.26 Å / Num. obs: 24255 / % possible obs: 99.4 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MUL

1mul


Resolution: 1.25→44.26 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 16.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1734 1229 5.1 %
Rwork0.1557 --
obs0.1565 24255 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms497 0 1 113 611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005513
X-RAY DIFFRACTIONf_angle_d0.888693
X-RAY DIFFRACTIONf_dihedral_angle_d8.959183
X-RAY DIFFRACTIONf_chiral_restr0.04786
X-RAY DIFFRACTIONf_plane_restr0.00390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.27720.24621370.24382614X-RAY DIFFRACTION98
1.2772-1.30690.26621410.22232592X-RAY DIFFRACTION98
1.3069-1.33960.30971360.20062619X-RAY DIFFRACTION99
1.3396-1.37580.24561650.18282592X-RAY DIFFRACTION99
1.3758-1.41630.19111560.17262617X-RAY DIFFRACTION99
1.4163-1.4620.1661390.15092637X-RAY DIFFRACTION99
1.462-1.51430.17011400.13172604X-RAY DIFFRACTION99
1.5143-1.57490.15931610.12182623X-RAY DIFFRACTION99
1.5749-1.64660.15921300.12442663X-RAY DIFFRACTION100
1.6466-1.73340.14961420.11932634X-RAY DIFFRACTION100
1.7334-1.8420.12971530.12862635X-RAY DIFFRACTION100
1.842-1.98430.1541250.13632661X-RAY DIFFRACTION100
1.9843-2.18390.17751460.12772637X-RAY DIFFRACTION100
2.1839-2.49990.1811370.13492664X-RAY DIFFRACTION100
2.4999-3.14950.17371250.17252666X-RAY DIFFRACTION100
3.1495-44.28770.16831310.17742672X-RAY DIFFRACTION100

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