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- PDB-3nr7: Crystal structure of S. typhimurium H-NS 1-83 -

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Basic information

Entry
Database: PDB / ID: 3nr7
TitleCrystal structure of S. typhimurium H-NS 1-83
ComponentsDNA-binding protein H-NS
KeywordsDNA BINDING PROTEIN / Dimer / oligomerisation / DNA condensation
Function / homology
Function and homology information


bent DNA binding / nucleoid / DNA-binding transcription repressor activity / negative regulation of gene expression, epigenetic / minor groove of adenine-thymine-rich DNA binding / protein-DNA complex / structural constituent of chromatin / protein dimerization activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription ...bent DNA binding / nucleoid / DNA-binding transcription repressor activity / negative regulation of gene expression, epigenetic / minor groove of adenine-thymine-rich DNA binding / protein-DNA complex / structural constituent of chromatin / protein dimerization activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / cytosol
Similarity search - Function
H-NS histone-like proteins / Histone-like protein H-NS, N-terminal / Histone-like protein H-NS, C-terminal domain superfamily / Histone-like protein H-NS / Histone-like protein H-NS, C-terminal domain / H-NS histone C-terminal domain / Domain in histone-like proteins of HNS family / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding protein H-NS
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsArold, S.T. / Leonard, P.G. / Parkinson, G.N. / Ladbury, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: H-NS forms a superhelical protein scaffold for DNA condensation.
Authors: Arold, S.T. / Leonard, P.G. / Parkinson, G.N. / Ladbury, J.E.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 H-NS
B: DNA-binding protein H-NS


Theoretical massNumber of molelcules
Total (without water)19,5922
Polymers19,5922
Non-polymers00
Water00
1
A: DNA-binding protein H-NS

B: DNA-binding protein H-NS


Theoretical massNumber of molelcules
Total (without water)19,5922
Polymers19,5922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_654y+1,-x+y,z-5/61
Buried area1700 Å2
ΔGint-13 kcal/mol
Surface area14140 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-23 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.397, 130.397, 55.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsTHE ASSEMBLY OF THE STRUCTURE IS A PSEUDO REPEAT OF THE DIMER DESCRIBED IN REMARK 350

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Components

#1: Protein DNA-binding protein H-NS / Histone-like protein HLP-II / Protein H1 / Protein B1


Mass: 9796.049 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-83 / Mutation: C21S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: H-NS, hns, hnsA, osmZ, STM1751 / Plasmid: pet14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P0A1S2

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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: 6.9 Å3/Da / Density % sol: 82.2 %
Crystal growTemperature: 290 K / Method: microdialysis / pH: 6.2
Details: 20 % (v/v) MPD, 20 mM phenol, 100 mM MES, pH 6.2, MICRODIALYSIS, temperature 290K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 17, 2006 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.7→32.6 Å / Num. all: 5676 / Num. obs: 5676 / % possible obs: 96.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 150 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.7
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / Num. unique all: 583 / % possible all: 96.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OV9

1ov9


Resolution: 3.7→32.6 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.93 / SU B: 119.068 / SU ML: 0.748 / Cross valid method: THROUGHOUT / ESU R Free: 0.578 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30375 427 7.5 %RANDOM
Rwork0.27107 ---
all0.27366 5676 --
obs0.27366 5676 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 189.256 Å2
Baniso -1Baniso -2Baniso -3
1-5.23 Å22.62 Å2-0 Å2
2--5.23 Å2-0 Å2
3----7.85 Å2
Refinement stepCycle: LAST / Resolution: 3.7→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 0 0 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221290
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9971732
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.59225.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.1315266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9751516
X-RAY DIFFRACTIONr_chiral_restr0.1150.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02952
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3771.5808
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73321292
X-RAY DIFFRACTIONr_scbond_it0.9843482
X-RAY DIFFRACTIONr_scangle_it1.854.5440
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.701→3.901 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.415 58 -
Rwork0.413 740 -
obs--94.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.8763-2.473310.653221.7359-10.561816.91430.02471.64842.10552.69180.6817-2.3914-2.668-0.2107-0.70641.40690.07590.94361.09120.55632.235164.456-22.1236.507
220.1108-4.407520.976817.0818-6.980826.613-0.8504-0.55211.5358-2.20250.26560.7736-2.4228-1.03720.58481.41090.04060.43130.5492-0.02711.076864.614-24.833-7.95
317.7987-4.2743-12.16689.0261-3.00637.21981.01030.5069-2.2873-0.83120.77771.48370.999-2.3182-1.7880.4088-0.49760.11240.5763-0.24571.147763.454-34.214-2.971
461.71931.60280.502718.8686-1.852652.25271.2783-2.3757-1.3582.1402-0.431-2.1995-0.16972.654-0.84730.35010.1583-0.08130.38590.16560.777868.008-32.1125.005
591.1819-0.0368-8.04039.21580.98493.37763.3312-1.398-0.6907-1.9346-1.7786-0.47071.81190.4551-1.55261.56360.43440.24891.4338-0.77741.496887.274-41.265-11.93
625.19856.0207-7.1256-0.8969-4.350619.84221.22623.01860.40430.95330.33631.0016-0.2606-1.3938-1.56260.89250.00831.05791.48680.22151.907944.992-40.56115.153
7-2.3998-16.729714.692932.2177-7.16412.2084.0199-2.6903-0.1467-0.4507-1.4838-0.2426-1.94650.4412-2.53611.8807-0.1111.43791.8595-0.50982.7685104.885-49.481-14.723
80.391919.6174-2.241319.29766.731-3.82623.15383.3421-1.32971.6461-0.3399-1.73111.3759-0.2132-2.8141.4377-0.29180.44662.98870.45862.036228.471-50.67718.969
9-53.1194-11.9535-40.6838.49644.1272-18.68284.28180.236-0.1528-3.625-0.5495-3.70873.57761.1816-3.73243.9410.4667-0.79813.55470.32763.4045111.072-43.759-24.491
1015.4838-9.55225.62543.4537-9.10230.6258-1.1871-1.5972-1.38081.5281.95880.1447-1.5996-1.808-0.77161.7313-0.18350.35322.13670.22162.837820.19-43.80425.489
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 21
2X-RAY DIFFRACTION2B2 - 21
3X-RAY DIFFRACTION3A22 - 41
4X-RAY DIFFRACTION4B22 - 41
5X-RAY DIFFRACTION5A42 - 56
6X-RAY DIFFRACTION6B42 - 56
7X-RAY DIFFRACTION7A57 - 69
8X-RAY DIFFRACTION8B57 - 69
9X-RAY DIFFRACTION9A70 - 83
10X-RAY DIFFRACTION10B70 - 83

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