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- PDB-4qju: Crystal structure of DNA-bound nucleoid associated protein, SAV1473 -

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Basic information

Entry
Database: PDB / ID: 4qju
TitleCrystal structure of DNA-bound nucleoid associated protein, SAV1473
Components
  • DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3')
  • DNA-binding protein HU
KeywordsDNA BINDING PROTEIN/DNA / DNA condensation / DNA BINDING PROTEIN-DNA complex
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 / DNA (> 10) / DNA-binding protein HU
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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

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Assembly

Deposited unit
A: DNA-binding protein HU
B: DNA-binding protein HU
C: DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3')
D: DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)34,1854
Polymers34,1854
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-68 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.468, 85.835, 92.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA-binding protein HU


Mass: 10713.167 Da / Num. of mol.: 2
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: DNA chain DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3')


Mass: 6379.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 17505 / Redundancy: 13.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 69.3
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 14.8 / Num. unique all: 834

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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: 4QJN

4qjn


Resolution: 2.16→29.076 Å / FOM work R set: 0.8077 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 880 5.04 %
Rwork0.1877 --
obs0.1907 17457 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.86 Å2 / Biso mean: 33.15 Å2 / Biso min: 16.69 Å2
Refinement stepCycle: LAST / Resolution: 2.16→29.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 847 0 219 2418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072319
X-RAY DIFFRACTIONf_angle_d1.2793291
X-RAY DIFFRACTIONf_dihedral_angle_d24.704948
X-RAY DIFFRACTIONf_chiral_restr0.064374
X-RAY DIFFRACTIONf_plane_restr0.004287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1603-2.29560.28551350.20332677X-RAY DIFFRACTION98
2.2956-2.47280.24721570.2042719X-RAY DIFFRACTION100
2.4728-2.72140.28411500.20682720X-RAY DIFFRACTION100
2.7214-3.11480.30221550.2072749X-RAY DIFFRACTION100
3.1148-3.92280.23381570.17432790X-RAY DIFFRACTION100
3.9228-29.07830.21521260.17822922X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -1.909 Å / Origin y: 8.3267 Å / Origin z: 19.483 Å
111213212223313233
T0.1479 Å20.0032 Å2-0.0082 Å2-0.1465 Å2-0.0012 Å2--0.1559 Å2
L0.179 °2-0.0298 °20.1172 °2-0.2011 °20.2578 °2--0.4489 °2
S-0.0018 Å °-0.0523 Å °0.0454 Å °0.0167 Å °-0.0445 Å °0.0651 Å °-0.0194 Å °0.0061 Å °0.0002 Å °
Refinement TLS groupSelection details: ALL

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