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- PDB-4qjn: Crystal structure of apo nucleoid associated protein, SAV1473 -

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Basic information

Entry
Database: PDB / ID: 4qjn
TitleCrystal structure of apo nucleoid associated protein, SAV1473
ComponentsDNA-binding protein HU
KeywordsDNA BINDING PROTEIN / DNA condensation / DNA binding
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 speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.613 Å
AuthorsLee, B.-J. / Kim, D.-H. / Im, H. / Yoon, H.-J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: beta-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism
Authors: Kim, D.-H. / Im, H. / Jee, J.-G. / Jang, S.-B. / Yoon, H.-J. / Kwon, A.-R. / Kang, S.-M. / Lee, B.-J.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,8534
Polymers42,8534
Non-polymers00
Water1,06359
1
A: DNA-binding protein HU
C: DNA-binding protein HU


Theoretical massNumber of molelcules
Total (without water)21,4262
Polymers21,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-38 kcal/mol
Surface area10840 Å2
MethodPISA
2
B: DNA-binding protein HU
D: DNA-binding protein HU


Theoretical massNumber of molelcules
Total (without water)21,4262
Polymers21,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-38 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.626, 82.938, 60.717
Angle α, β, γ (deg.)90.00, 94.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA-binding protein HU


Mass: 10713.167 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: hup / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99U17
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG2000 monomethyl ether, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 18, 2011
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 10877 / Redundancy: 6 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 33.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 7.2 / Num. unique all: 474

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HUU

1huu


Resolution: 2.613→30.248 Å / FOM work R set: 0.7466 / SU ML: 0.31 / σ(F): 0 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 1047 10.02 %RANDOM
Rwork0.2068 ---
obs0.2124 10451 94.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.91 Å2 / Biso mean: 41.78 Å2 / Biso min: 14.46 Å2
Refinement stepCycle: LAST / Resolution: 2.613→30.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 59 2763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092728
X-RAY DIFFRACTIONf_angle_d1.3483648
X-RAY DIFFRACTIONf_chiral_restr0.094412
X-RAY DIFFRACTIONf_plane_restr0.007484
X-RAY DIFFRACTIONf_dihedral_angle_d10.9961056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6125-2.75020.32321270.25131175130283
2.7502-2.92240.33621470.26951277142492
2.9224-3.14780.30361500.24171344149495
3.1478-3.46410.29721560.21721386154298
3.4641-3.96450.22271570.19511399155698
3.9645-4.99120.24281560.18111392154898
4.9912-30.250.24891540.19391431158598

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