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- PDB-5b52: Crystal structure of the N-terminal domain of H-NS family protein TurB -

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Basic information

Entry
Database: PDB / ID: 5b52
TitleCrystal structure of the N-terminal domain of H-NS family protein TurB
ComponentsH-NS family protein MvaT
KeywordsTRANSCRIPTION / transcriptional regulator / nucleoid associated protein
Function / homologyMvaT, DNA-binding domain / Bacterial xenogeneic silencer MvaT, C-terminal domain / H-NS family protein MvaT
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSuzuki-Minakuchi, C. / Nojiri, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Kato Memorial Bioscience Foundation Japan
CitationJournal: Febs Lett. / Year: 2016
Title: Structural similarities and differences in H-NS family proteins revealed by the N-terminal structure of TurB in Pseudomonas putida KT2440
Authors: Suzuki-Minakuchi, C. / Kawazuma, K. / Matsuzawa, J. / Vasileva, D. / Fujimoto, Z. / Terada, T. / Okada, K. / Nojiri, H.
History
DepositionApr 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-NS family protein MvaT
B: H-NS family protein MvaT


Theoretical massNumber of molelcules
Total (without water)16,0092
Polymers16,0092
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-20 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.555, 143.350, 75.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-110-

HOH

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Components

#1: Protein H-NS family protein MvaT / Transcriptional regulator MvaT


Mass: 8004.292 Da / Num. of mol.: 2 / Fragment: UNP residues 1-61 / Mutation: R8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain KT2440) (bacteria)
Strain: KT2440 / Gene: PP_3765 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q88GF9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, BIS-TRIS propane / PH range: 6.9-7.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NE3A11
SYNCHROTRONPhoton Factory AR-NE3A20.9644
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDNov 24, 2014
ADSC QUANTUM 2702CCDNov 24, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.96441
Reflection

Entry-ID: 5B52

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.3-100789299.613.90.048157.2
2.8-100448699.813.80.09232.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.3813.40.6324.11100
2.8-2.913.10.9762.72100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data processing
RefinementMethod to determine structure: SAD / Resolution: 2.3→52.03 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.811 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29624 344 4.6 %RANDOM
Rwork0.24178 ---
obs0.24457 7109 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å20 Å2
2---0.21 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→52.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 0 48 955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019913
X-RAY DIFFRACTIONr_bond_other_d0.0010.02947
X-RAY DIFFRACTIONr_angle_refined_deg1.9222.021217
X-RAY DIFFRACTIONr_angle_other_deg0.8632187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16926.31638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54315194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.068154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02171
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1683.924466
X-RAY DIFFRACTIONr_mcbond_other4.0843.921465
X-RAY DIFFRACTIONr_mcangle_it6.3165.845579
X-RAY DIFFRACTIONr_mcangle_other6.3155.853580
X-RAY DIFFRACTIONr_scbond_it5.6154.63447
X-RAY DIFFRACTIONr_scbond_other5.6094.635448
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.4036.661639
X-RAY DIFFRACTIONr_long_range_B_refined11.67129.5661029
X-RAY DIFFRACTIONr_long_range_B_other11.68629.5231024
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 23 -
Rwork0.29 419 -
obs--77.54 %

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