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- PDB-4icg: N-terminal dimerization domain of H-NS in complex with Hha (Salmo... -

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Basic information

Entry
Database: PDB / ID: 4icg
TitleN-terminal dimerization domain of H-NS in complex with Hha (Salmonella Typhimurium)
Components
  • DNA-binding protein H-NS
  • Hemolysin expression modulating protein (Involved in environmental regulation of virulence factors)
KeywordsDNA BINDING PROTEIN / Hha
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
HHA / Haemolysin expression modulating, HHA / HHA superfamily / Haemolysin expression modulating protein / 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 ...HHA / Haemolysin expression modulating, HHA / HHA superfamily / Haemolysin expression modulating protein / 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 / Monooxygenase / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding protein H-NS / Hemolysin expression-modulating protein Hha
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9217 Å
AuthorsAli, S.S. / Whitney, J.C. / Stevenson, J. / Robinson, H. / Howell, P.L. / Navarre, W.W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Insights into the Regulation of Foreign Genes in Salmonella by the Hha/H-NS Complex.
Authors: Ali, S.S. / Whitney, J.C. / Stevenson, J. / Robinson, H. / Howell, P.L. / Navarre, W.W.
History
DepositionDec 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2May 29, 2013Group: Database references
Revision 1.3May 18, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA-binding protein H-NS
C: Hemolysin expression modulating protein (Involved in environmental regulation of virulence factors)
A: DNA-binding protein H-NS
D: Hemolysin expression modulating protein (Involved in environmental regulation of virulence factors)


Theoretical massNumber of molelcules
Total (without water)29,0224
Polymers29,0224
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.880, 82.900, 47.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 5459.920 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: S2G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: hns, hnsA, osmZ, STM1751, STMUK_1724 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A1S2
#2: Protein Hemolysin expression modulating protein (Involved in environmental regulation of virulence factors)


Mass: 9050.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: hha, STM0473, STMUK_0480 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CR17

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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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2012
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 7129 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9217→47.13 Å / SU ML: 0.55 / σ(F): 0 / Phase error: 38.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3315 626 10.12 %Random
Rwork0.2772 ---
all0.2829 6183 --
obs0.2829 6183 88.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9217→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 0 0 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071704
X-RAY DIFFRACTIONf_angle_d1.062312
X-RAY DIFFRACTIONf_dihedral_angle_d14.174612
X-RAY DIFFRACTIONf_chiral_restr0.067282
X-RAY DIFFRACTIONf_plane_restr0.004299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9217-3.21570.4379920.3741826X-RAY DIFFRACTION54
3.2157-3.68090.38471690.32811522X-RAY DIFFRACTION98
3.6809-4.63690.31031720.25761554X-RAY DIFFRACTION99
4.6369-47.13610.31061930.25411655X-RAY DIFFRACTION100
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)
16.9549-0.15871.79913.0756-1.24522.72080.4372-0.2232-0.1411-0.8438-0.0295-0.0891-0.1022-0.4102-0.08690.43480.01710.0180.40550.13260.4592-63.320312.545160.6555
23.64390.4955-0.49171.01520.31343.6699-0.36480.11730.0942-0.12450.17930.60210.2321-0.2867-0.78560.24350.0018-0.13780.26670.24140.9285-63.894912.054560.496
34.4603-1.48141.44613.41052.19534.22460.1035-0.34770.54510.3235-0.1494-0.84870.35830.4913-0.11040.51570.2130.14090.77990.25150.5326-46.247610.734270.1232
45.0441-2.09150.90173.7380.14734.24-0.27281.1823-0.0562-0.16570.53830.3024-0.0224-0.68950.03690.5707-0.1843-0.26310.98650.48280.8233-75.780116.934146.2357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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