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- PDB-8h8h: Crystal structure of the N-terminal domain of H-NS family protein... -

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Basic information

Entry
Database: PDB / ID: 8h8h
TitleCrystal structure of the N-terminal domain of H-NS family protein TurB (TurB_nt50)
ComponentsH-NS family protein MvaT
KeywordsTRANSCRIPTION / nucleoid-associated protein
Function / homologyMvaT, DNA-binding domain / H-NS family protein MvaT
Function and homology information
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsVasileva, D. / Suzuki-Minakuchi, C. / Arakawa, T. / Nojiri, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K05408 Japan
Japan Society for the Promotion of Science (JSPS)21H02097 Japan
Japan Science and TechnologyJPMJER1502 Japan
CitationJournal: To Be Published
Title: Crystal structure of the N-terminal domain of H-NS family protein TurB (TurB_nt50)
Authors: Vasileva, D. / Suzuki-Minakuchi, C. / Arakawa, T. / Nojiri, H.
History
DepositionOct 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: H-NS family protein MvaT
D: H-NS family protein MvaT
E: H-NS family protein MvaT
F: H-NS family protein MvaT
G: H-NS family protein MvaT
H: H-NS family protein MvaT


Theoretical massNumber of molelcules
Total (without water)54,7198
Polymers54,7198
Non-polymers00
Water23413
1
A: H-NS family protein MvaT
G: H-NS family protein MvaT


Theoretical massNumber of molelcules
Total (without water)13,6802
Polymers13,6802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-15 kcal/mol
Surface area8490 Å2
MethodPISA
2
B: H-NS family protein MvaT
F: H-NS family protein MvaT


Theoretical massNumber of molelcules
Total (without water)13,6802
Polymers13,6802
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-15 kcal/mol
Surface area8600 Å2
MethodPISA
3
C: H-NS family protein MvaT
E: H-NS family protein MvaT


Theoretical massNumber of molelcules
Total (without water)13,6802
Polymers13,6802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-16 kcal/mol
Surface area8660 Å2
MethodPISA
4
D: H-NS family protein MvaT
H: H-NS family protein MvaT


Theoretical massNumber of molelcules
Total (without water)13,6802
Polymers13,6802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-16 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.692, 63.303, 275.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
H-NS family protein MvaT


Mass: 6839.878 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria)
Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
Gene: PP_3765 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88GF9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.65 Å3/Da / Density % sol: 71.3 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: PEG 3350, HEPES, ammonium acetate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
1951N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NE3A11
SYNCHROTRONPhoton Factory BL-1A22.7
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M-F1PIXELJun 9, 2018
DECTRIS EIGER X 4M2PIXELJul 2, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.71
Reflection

Biso Wilson estimate: 59.61 Å2 / Entry-ID: 8H8H / Rrim(I) all: 0.146

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.7-46.642293698.9213.10.140.041110.9
3-137.21691296.2200.1440.024221.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible allRrim(I) all
2.7-2.8313.81.3552.422310.9560.375198.75
3-3.180.4715.524470.9960.095292.40.481

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSJan 10, 2022data reduction
AimlessCCP4Interface 8.0data scaling
CRANK2CCP4Interface 7.0phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→40.92 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 2270 10 %
Rwork0.2465 --
obs0.2505 22702 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 0 13 3255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093258
X-RAY DIFFRACTIONf_angle_d1.0744301
X-RAY DIFFRACTIONf_dihedral_angle_d5.577428
X-RAY DIFFRACTIONf_chiral_restr0.046466
X-RAY DIFFRACTIONf_plane_restr0.008553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.53591400.42711237X-RAY DIFFRACTION99
2.76-2.820.45761470.39451201X-RAY DIFFRACTION98
2.82-2.890.39161310.36951292X-RAY DIFFRACTION99
2.89-2.970.37471350.32921208X-RAY DIFFRACTION98
2.97-3.060.37771370.32031258X-RAY DIFFRACTION97
3.06-3.160.42481260.32661232X-RAY DIFFRACTION97
3.16-3.270.4221370.33151281X-RAY DIFFRACTION98
3.27-3.40.30331180.28861254X-RAY DIFFRACTION100
3.4-3.560.29221770.26131262X-RAY DIFFRACTION100
3.56-3.740.3121590.24951253X-RAY DIFFRACTION100
3.74-3.980.32181220.24961307X-RAY DIFFRACTION100
3.98-4.280.34011340.22611299X-RAY DIFFRACTION100
4.29-4.720.23861410.21351292X-RAY DIFFRACTION100
4.72-5.40.24271480.2051313X-RAY DIFFRACTION100
5.4-6.790.29121570.24751330X-RAY DIFFRACTION100
6.8-40.920.1521610.1681413X-RAY DIFFRACTION99

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