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- PDB-1yg2: Structure of the Vibrio cholerae virulence activator AphA -

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Basic information

Entry
Database: PDB / ID: 1yg2
TitleStructure of the Vibrio cholerae virulence activator AphA
Componentsgene activator AphA
KeywordsTRANSCRIPTION / virulence factor / vibrio cholerae / winged helix / transcription factor
Function / homology
Function and homology information


Helix Hairpins - #190 / Transcription regulator PadR, C-terminal / Virulence activator alpha C-term / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A ...Helix Hairpins - #190 / Transcription regulator PadR, C-terminal / Virulence activator alpha C-term / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PadR family transcriptional regulator
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsDe Silva, R.S. / Kovacikova, G. / Lin, W. / Taylor, R.T. / Skorupski, K. / Kull, F.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of the virulence gene activator AphA from Vibrio cholerae reveals it is a novel member of the winged helix transcription factor superfamily
Authors: De Silva, R.S. / Kovacikova, G. / Lin, W. / Taylor, R.K. / Skorupski, K. / Kull, F.J.
History
DepositionJan 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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: gene activator AphA


Theoretical massNumber of molelcules
Total (without water)20,4531
Polymers20,4531
Non-polymers00
Water1,60389
1
A: gene activator AphA

A: gene activator AphA


Theoretical massNumber of molelcules
Total (without water)40,9062
Polymers40,9062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6630 Å2
ΔGint-45 kcal/mol
Surface area16390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.500, 94.650, 59.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Detailsbiological unit is a dimer

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Components

#1: Protein gene activator AphA / hypothetical protein VC2647


Mass: 20453.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 serogroup O1 / Gene: AphA / Plasmid: pWEL18 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9X399
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.628 Å3/Da / Density % sol: 51.39 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.3
Details: MES, magenesium sulphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONNSLS X6A20.98
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEJul 1, 2003
ADSC QUANTUM 42CCDJun 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.981
ReflectionResolution: 2.2→42.29 Å / Num. all: 11425 / Num. obs: 11425 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.1 Å2 / Rsym value: 0.063
Reflection shellResolution: 2.2→2.4 Å / Rsym value: 0.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCdata collection
XDSdata reduction
CNS1.1refinement
XDSdata scaling
CNS1.1phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→42.29 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2458693.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 572 5 %RANDOM
Rwork0.233 ---
obs0.2331 11425 99.5 %-
all-11425 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.0045 Å2 / ksol: 0.369205 e/Å3
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1--8.29 Å20 Å20 Å2
2--2.1 Å20 Å2
3---6.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 0 89 1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it2.622
X-RAY DIFFRACTIONc_scangle_it4.072.5
LS refinement shellResolution: 2.2→2.4 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 93 5 %
Rwork0.273 1752 -
obs-17406 99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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