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- PDB-1b8z: HU FROM THERMOTOGA MARITIMA -

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Basic information

Entry
Database: PDB / ID: 1b8z
TitleHU FROM THERMOTOGA MARITIMA
ComponentsPROTEIN (HISTONELIKE PROTEIN HU)
KeywordsDNA BINDING PROTEIN / THERMOTOGA MARITIMA / THERMOSTABLE DNA BINDING PROTEIN
Function / homology
Function and homology information


chromosome condensation / structural constituent of chromatin / DNA 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
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChristodoulou, E. / Rypniewski, W.R. / Vorgias, C.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Cloning, overproduction, purification and crystallization of the DNA binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima.
Authors: Christodoulou, E. / Vorgias, C.E.
History
DepositionFeb 3, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (HISTONELIKE PROTEIN HU)
B: PROTEIN (HISTONELIKE PROTEIN HU)


Theoretical massNumber of molelcules
Total (without water)20,0362
Polymers20,0362
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-38 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.120, 46.120, 77.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein PROTEIN (HISTONELIKE PROTEIN HU)


Mass: 10018.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P36206
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMNa-phosphate1drop
380 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8833
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8833 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 21552 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.82 Å2 / Rsym value: 5.6 / Net I/σ(I): 19.1
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 59 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.59

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1078 5 %RANDOM
Rwork0.215 ---
obs-21554 99.9 %-
Displacement parametersBiso mean: 27.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 0 77 1117
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0220.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8293
X-RAY DIFFRACTIONp_mcangle_it2.6965
X-RAY DIFFRACTIONp_scbond_it4.6266
X-RAY DIFFRACTIONp_scangle_it6.9548
X-RAY DIFFRACTIONp_plane_restr0.01510.03
X-RAY DIFFRACTIONp_chiral_restr0.0890.03
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2690.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1370.3
X-RAY DIFFRACTIONp_planar_tor2.425
X-RAY DIFFRACTIONp_staggered_tor13.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor13.120
X-RAY DIFFRACTIONp_special_tor20

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