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- PDB-5eka: HU DNA-binding protein from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5eka
TitleHU DNA-binding protein from Thermus thermophilus
ComponentsDNA-binding protein HU
KeywordsDNA BINDING PROTEIN / HU PROTEIN / HISTONE-LIKE PROTEIN / 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 speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsPapageorgiou, A. / Adam, P. / Stavros, P. / Nounesis, G. / Meijers, R. / Petratos, K. / Vorgias, C.E.
CitationJournal: Extremophiles / Year: 2016
Title: HU histone-like DNA-binding protein from Thermus thermophilus: structural and evolutionary analyses.
Authors: Papageorgiou, A.C. / Adam, P.S. / Stavros, P. / Nounesis, G. / Meijers, R. / Petratos, K. / Vorgias, C.E.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 10, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4372
Polymers10,3451
Non-polymers921
Water1,72996
1
A: DNA-binding protein HU
hetero molecules

A: DNA-binding protein HU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8754
Polymers20,6912
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4980 Å2
ΔGint-45 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.464, 38.432, 44.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-263-

HOH

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Components

#1: Protein DNA-binding protein HU / DNA-binding protein II / TL29


Mass: 10345.323 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DNA-binding protein HU from Thermus thermophilus. UniProtKB code: DBH_THET8
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1349 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19436
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.3 Å3/Da / Density % sol: 51 % / Description: Rod-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: Protein solutions of 14-18 mg/ml, Buffer: 0.2 M Na-formate, Precipitating agent: 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97631 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2015 / Details: BIMORPH MIRRORS
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 1.69→44.9 Å / Num. obs: 10742 / % possible obs: 96.3 % / Redundancy: 12 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.073 / Net I/av σ(I): 17.6 / Net I/σ(I): 22.6
Reflection shellResolution: 1.69→1.74 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3 / % possible all: 59.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B8Z

1b8z


Resolution: 1.69→44.86 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.387 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25612 534 5 %RANDOM
Rwork0.19776 ---
obs0.20077 10208 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0 Å2
2---1.01 Å2-0 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.69→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms644 0 6 96 746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02664
X-RAY DIFFRACTIONr_bond_other_d0.0020.02727
X-RAY DIFFRACTIONr_angle_refined_deg1.4772.009883
X-RAY DIFFRACTIONr_angle_other_deg0.75931680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.011583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35324.28621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25215143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.624154
X-RAY DIFFRACTIONr_chiral_restr0.0790.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02125
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0291.452338
X-RAY DIFFRACTIONr_mcbond_other1.0131.446337
X-RAY DIFFRACTIONr_mcangle_it1.592.164419
X-RAY DIFFRACTIONr_mcangle_other1.5932.169420
X-RAY DIFFRACTIONr_scbond_it1.9291.845324
X-RAY DIFFRACTIONr_scbond_other1.9291.845324
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1042.621465
X-RAY DIFFRACTIONr_long_range_B_refined7.47213.452764
X-RAY DIFFRACTIONr_long_range_B_other7.412.523736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.694→1.738 Å
RfactorNum. reflection% reflection
Rfree0.23 27 -
Rwork0.23 454 -
obs--59.6 %
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)
11.04780.1245-0.215.3839-0.43840.93720.0364-0.0699-0.04270.3428-0.15990.097-0.02030.00780.12340.0229-0.01440.0070.1023-0.01170.022-1.871-0.0973.892
20.3061-0.06191.50550.0215-0.27848.58680.16430.1368-0.09-0.0883-0.01640.0020.43340.2363-0.14790.46760.091-0.02110.3623-0.07770.3477-1.76213.397-23.316
315.2443.63396.80991.98912.22363.3633-0.2150.3602-0.0581-0.32820.23190.008-0.24490.2321-0.01680.2381-0.01570.00050.20250.0250.1688-8.25515.415-22.924
46.272-7.37232.046811.1458-2.51883.76530.33680.1014-0.2068-0.6386-0.18690.05990.27320.2073-0.150.04950.02480.0020.1131-0.01330.05885.469-3.576-9.244
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 59
2X-RAY DIFFRACTION2A60 - 64
3X-RAY DIFFRACTION3A76 - 78
4X-RAY DIFFRACTION4A79 - 96

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