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- PDB-1riy: HU mutant V42I from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1riy
TitleHU mutant V42I from Thermotoga maritima
ComponentsHu DNA-binding protein
KeywordsDNA BINDING PROTEIN / HISTONE-LIKE PROTEIN / THERMOSTABLE DNA-BINDING PROTEIN / HU PROTEIN MUTANT V42I / THERMOTOGA MARITIMA
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: 1.8 Å
AuthorsKavounis, C. / Petratos, K. / Tucker, P. / Vorgias, C.E.
CitationJournal: To be Published
Title: The structure of the DNA binding protein HU Thermotoga maritima with a single conservative substitution (V42I) that confers significant destabilisation
Authors: Kavounis, C. / Petratos, K. / Tucker, P. / Vorgias, C.E.
History
DepositionNov 18, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hu DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,0321
Polymers10,0321
Non-polymers00
Water63135
1
A: Hu DNA-binding protein

A: Hu DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)20,0642
Polymers20,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3740 Å2
ΔGint-40 kcal/mol
Surface area7450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)45.447, 45.447, 76.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe second molecule of the biological dimer is generated by the two fold axis: 1-y, 1-x, 1/2-z.

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Components

#1: Protein Hu DNA-binding protein / Histone-like DNA binding protein


Mass: 10032.128 Da / Num. of mol.: 1 / Mutation: V42I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: HUP / Plasmid: pET-11a-HUTmar / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36206
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.3
Details: 100mM Na-acetate, pH 4.0-4.5, 80-90% saturated ammonium sulphate, pH 4.3, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0727 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 16, 2001 / Details: Bent mirror
RadiationMonochromator: Double crystal focussing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0727 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 59041 / Num. obs: 7873 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 28.105 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 16.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.9 / Num. unique all: 376 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B8Z

1b8z


Resolution: 1.8→15.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.297 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Anisotropic TLS refinement / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.142 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2859 360 4.6 %RANDOM
Rwork0.21615 ---
all0.21922 7832 --
obs0.21922 7472 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20 Å2
2--1.16 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms517 0 0 35 552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022520
X-RAY DIFFRACTIONr_bond_other_d0.0010.02528
X-RAY DIFFRACTIONr_angle_refined_deg1.3552.005692
X-RAY DIFFRACTIONr_angle_other_deg0.88231223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.676369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95315113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02551
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0286
X-RAY DIFFRACTIONr_nbd_refined0.2330.3104
X-RAY DIFFRACTIONr_nbd_other0.2120.3413
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.527
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.32
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.319
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9381.5349
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7262555
X-RAY DIFFRACTIONr_scbond_it3.1983171
X-RAY DIFFRACTIONr_scangle_it5.6864.5137
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 25 -
Rwork0.221 537 -
obs-537 100 %
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)
10.99080.159-0.19931.5260.66721.4001-0.02620.069-0.09180.1078-0.04390.04620.0085-0.01890.070.0410.0033-0.01380.0686-0.0160.111927.26715.92519.724
211.50872.453-9.29933.3752-3.761418.3413-0.46880.49880.4579-0.16410.06160.1667-0.2738-0.62180.40710.1054-0.0089-0.10130.05420.0310.106823.63130.23215.571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 541 - 54
2X-RAY DIFFRACTION2AA74 - 9074 - 90

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