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- PDB-8hd5: The crystal structure of Hu protein in Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 8hd5
TitleThe crystal structure of Hu protein in Staphylococcus aureus
ComponentsDNA-binding protein HU
KeywordsDNA BINDING PROTEIN / protein structure / bacterial protein
Function / homology
Function and homology information


chromosome condensation / structural constituent of chromatin / DNA binding
Similarity search - Function
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
Similarity search - Domain/homology
DNA-binding protein HU
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsLiu, Y.H. / Chen, H. / Li, Y. / Liu, B.
Funding support China, 1items
OrganizationGrant numberCountry
China Postdoctoral Science Foundation2020M682420 China
CitationJournal: To Be Published
Title: The crystal structure of Hu protein in Staphylococcus aureus
Authors: Liu, Y.H. / Li, Y. / Liu, B.
History
DepositionNov 3, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein HU
C: DNA-binding protein HU
B: DNA-binding protein HU
D: DNA-binding protein HU


Theoretical massNumber of molelcules
Total (without water)38,5684
Polymers38,5684
Non-polymers00
Water3,369187
1
A: DNA-binding protein HU
C: DNA-binding protein HU


Theoretical massNumber of molelcules
Total (without water)19,2842
Polymers19,2842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-39 kcal/mol
Surface area10960 Å2
MethodPISA
2
B: DNA-binding protein HU
D: DNA-binding protein HU


Theoretical massNumber of molelcules
Total (without water)19,2842
Polymers19,2842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-37 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.427, 82.369, 61.633
Angle α, β, γ (deg.)90.000, 93.160, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
DNA-binding protein HU


Mass: 9642.015 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Gene: hup, SAV1473
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpGUT1 (others)
References: UniProt: Q99U17
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.14→29.19 Å / Num. obs: 22347 / % possible obs: 97.95 % / Redundancy: 2 % / Biso Wilson estimate: 41.23 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.62
Reflection shellResolution: 2.14→2.22 Å / Num. unique obs: 2190 / CC1/2: 0.819

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QJN

4qjn


Resolution: 2.14→29.19 Å / SU ML: 0.2732 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.1669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2624 1090 4.89 %
Rwork0.1972 21219 -
obs0.2002 22309 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.21 Å2
Refinement stepCycle: LAST / Resolution: 2.14→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 187 2891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772728
X-RAY DIFFRACTIONf_angle_d0.8753648
X-RAY DIFFRACTIONf_chiral_restr0.0544412
X-RAY DIFFRACTIONf_plane_restr0.0076484
X-RAY DIFFRACTIONf_dihedral_angle_d13.8791372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.240.28891570.27662602X-RAY DIFFRACTION97.42
2.24-2.360.29611080.24782632X-RAY DIFFRACTION97.2
2.36-2.510.25981320.23122635X-RAY DIFFRACTION97.77
2.51-2.70.28181550.2232617X-RAY DIFFRACTION97.85
2.7-2.970.33291350.23242679X-RAY DIFFRACTION98.39
2.97-3.40.30481490.21562651X-RAY DIFFRACTION98.66
3.4-4.280.24631340.17852673X-RAY DIFFRACTION98.49
4.28-29.190.21411200.16462730X-RAY DIFFRACTION98.21

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