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- PDB-2fgt: Crystal Structure of YycH from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2fgt
TitleCrystal Structure of YycH from Bacillus subtilis
ComponentsTwo-component system yycF/yycG regulatory protein yycHTwo-component regulatory system
KeywordsSIGNALING PROTEIN / signal transduction / YycH / calcium binding / beta sheet
Function / homology
Function and homology information


membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Nuclear Transport Factor 2; Chain: A, - #310 / Regulatory protein YycH / YycH protein / YycH protein, domain 2 / Regulatory protein YycH/YycI , domain 2 / TATA-Binding Protein / Nuclear Transport Factor 2; Chain: A, / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Two-component system WalR/WalK regulatory protein YycH
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSzurmant, H. / Zhao, H. / Mohan, M.A. / James, H.A. / Varughese, K.I.
CitationJournal: Protein Sci. / Year: 2006
Title: The crystal structure of YycH involved in the regulation of the essential YycFG two-component system in Bacillus subtilis reveals a novel tertiary structure.
Authors: Szurmant, H. / Zhao, H. / Mohan, M.A. / Hoch, J.A. / Varughese, K.I.
History
DepositionDec 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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

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Assembly

Deposited unit
A: Two-component system yycF/yycG regulatory protein yycH


Theoretical massNumber of molelcules
Total (without water)47,9441
Polymers47,9441
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.578, 63.578, 192.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Two-component system yycF/yycG regulatory protein yycH / Two-component regulatory system


Mass: 47943.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: JH642 / Gene: yycH / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q794W0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 0.1 M Tris_HCl, 18% PEG 3350, 100 mM calcium acetate, pH 7.0, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.01978, 0.97958, 0.97625
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 20, 2005
RadiationMonochromator: Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.019781
20.979581
30.976251
ReflectionResolution: 2.3→38.35 Å / Num. all: 18254 / Num. obs: 18254 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4 / Num. unique all: 1781 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
SCALAdata scaling
SOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→38.35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1800 -random
Rwork0.251 ---
all0.255 18390 --
obs0.255 18254 99.2 %-
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 0 94 3058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.398 306 -
Rwork0.269 --
obs-2688 100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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