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- PDB-5l8z: Structure of thermostable DNA-binding HU protein from micoplasma ... -

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Basic information

Entry
Database: PDB / ID: 5l8z
TitleStructure of thermostable DNA-binding HU protein from micoplasma Spiroplasma melliferum
ComponentsDNA-binding protein
KeywordsDNA BINDING PROTEIN / thermostable / DNA-binding / HU-protein / Spiroplasma melliferum / histone-like / NAP
Function / homology
Function and homology information


structural constituent of chromatin / DNA binding
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
Biological speciesSpiroplasma melliferum KC3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsBoyko, K.M. / Gorbacheva, M.A. / Rakitina, T.V. / Korzhenevskiy, D.A. / Kamashev, D.E. / Vanyushkina, A.A. / Lipkin, A.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation15-14-00063 Russian Federation
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis of the high thermal stability of the histone-like HU protein from the mollicute Spiroplasma melliferum KC3.
Authors: Boyko, K.M. / Rakitina, T.V. / Korzhenevskiy, D.A. / Vlaskina, A.V. / Agapova, Y.K. / Kamashev, D.E. / Kleymenov, S.Y. / Popov, V.O.
History
DepositionJun 9, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionJun 22, 2016ID: 5CVX
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4292
Polymers10,4061
Non-polymers231
Water2,234124
1
A: DNA-binding protein
hetero molecules

A: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8584
Polymers20,8122
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4650 Å2
ΔGint-58 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.000, 39.010, 38.780
Angle α, β, γ (deg.)90.000, 108.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

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Components

#1: Protein DNA-binding protein


Mass: 10405.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiroplasma melliferum KC3 (bacteria) / Gene: SPM_000560 / Plasmid: pET-21d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A037USE5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M TRIS, 35% PEG400, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.984 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 22, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.4→31.64 Å / Num. obs: 15292 / % possible obs: 95.4 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.03 / Rrim(I) all: 0.058 / Net I/σ(I): 13.5 / Num. measured all: 54665 / Scaling rejects: 47
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.279 / % possible all: 96.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HUU

1huu


Resolution: 1.4→31.64 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.153 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0722 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.074 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 724 4.7 %RANDOM
Rwork0.18 ---
obs0.1815 14567 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 48.78 Å2 / Biso mean: 17.707 Å2 / Biso min: 8.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å2-0.19 Å2
2---0.02 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: final / Resolution: 1.4→31.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms704 0 1 124 829
Biso mean--17.06 27.26 -
Num. residues----93
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019741
X-RAY DIFFRACTIONr_angle_refined_deg2.2291.956985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80125.45533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05315153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.564153
X-RAY DIFFRACTIONr_chiral_restr0.1230.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02535
X-RAY DIFFRACTIONr_mcbond_it1.7081.559376
X-RAY DIFFRACTIONr_mcangle_it2.4092.324467
X-RAY DIFFRACTIONr_scbond_it2.4181.713365
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 50 -
Rwork0.231 1104 -
all-1154 -
obs--96.25 %

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