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- PDB-1mul: Crystal structure of the E. coli HU alpha2 protein -

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Basic information

Entry
Database: PDB / ID: 1mul
TitleCrystal structure of the E. coli HU alpha2 protein
ComponentsDNA binding protein HU-alpha
KeywordsDNA BINDING PROTEIN / histone-like
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-binding protein HU-alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRamstein, J. / Hervouet, N. / Coste, F. / Zelwer, C. / Oberto, J. / Castaing, B.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Evidence of a Thermal Unfolding Dimeric Intermediate for the Escherichia coli Histone-like HU Proteins: Thermodynamics and Structure.
Authors: Ramstein, J. / Hervouet, N. / Coste, F. / Zelwer, C. / Oberto, J. / Castaing, B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray diffraction analysis of the homodimeric form alpha2 of the HU protein from E. coli
Authors: Coste, F. / Hervouet, N. / Oberto, J. / Zelwer, C. / Castaing, B.
History
DepositionSep 24, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)9,5501
Polymers9,5501
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA binding protein HU-alpha

A: DNA binding protein HU-alpha


Theoretical massNumber of molelcules
Total (without water)19,1002
Polymers19,1002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3450 Å2
ΔGint-36 kcal/mol
Surface area7850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)31.090, 55.340, 117.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


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 / Plasmid: pJEShupA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0ACF0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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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: 3.07 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Coste, F., (1999) Acta Cryst., D55, 1952.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→32 Å / Num. all: 4755 / Num. obs: 4607 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.056 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 344 / Rsym value: 0.161
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS0.5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 983947.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 485 10.5 %RANDOM
Rwork0.234 ---
all0.256 4755 --
obs0.234 4607 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.2065 Å2 / ksol: 0.358714 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.15 Å20 Å20 Å2
2--8.06 Å20 Å2
3---1.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms539 0 0 50 589
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 73 10 %
Rwork0.267 660 -
obs--94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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