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- PDB-4r6i: AtxA protein, a virulence regulator from Bacillus anthracis. -

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Basic information

Entry
Database: PDB / ID: 4r6i
TitleAtxA protein, a virulence regulator from Bacillus anthracis.
ComponentsAnthrax toxin expression trans-acting positive regulator
KeywordsTRANSCRIPTION / structural genomics / IDP01169 / AtxA / transcriptional activator / virulence regulator / DNA binding / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / regulation of DNA-templated transcription
Similarity search - Function
Mga helix-turn-helix domain / Mga helix-turn-helix domain / PRD domain / PRD domain / PRD domain superfamily / PRD domain profile. / Helix-turn-helix, type 11 / HTH domain / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Anthrax toxin expression trans-acting positive regulator
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsOsipiuk, J. / Horton, L.B. / Koehler, T.M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Mol.Microbiol. / Year: 2015
Title: Crystal structure of Bacillus anthracis virulence regulator AtxA and effects of phosphorylated histidines on multimerization and activity.
Authors: Hammerstrom, T.G. / Horton, L.B. / Swick, M.C. / Joachimiak, A. / Osipiuk, J. / Koehler, T.M.
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anthrax toxin expression trans-acting positive regulator
B: Anthrax toxin expression trans-acting positive regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6774
Polymers112,6562
Non-polymers1,0212
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-10 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.460, 135.167, 180.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Anthrax toxin expression trans-acting positive regulator


Mass: 56327.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: atxA, BXA0146, GBAA_pXO1_0146, pXO1-119 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44636
#2: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.54 Å3/Da / Density % sol: 65.25 % / Mosaicity: 0.37 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3 M NaCL, 0.1 M Bis-Tris buffer, 0.2% N-dodecyl-beta-D-maltoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→46.93 Å / Num. all: 46330 / Num. obs: 46330 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 78.2 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.703 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRpim(I) allRrim(I) allΧ2% possible all
2.65-2.76.70.8942.1722500.3670.9680.97699.9
2.7-2.746.70.74422890.3050.8050.95999.8
2.74-2.86.70.59422860.2440.6430.98999.9
2.8-2.856.70.52423160.2150.5671.00999.9
2.85-2.926.70.41822890.1710.4531.03799.9
2.92-2.986.70.34522990.1420.3731.067100
2.98-3.066.70.29622970.1220.3211.092100
3.06-3.146.70.23322990.0960.2521.137100
3.14-3.236.70.18823250.0770.2031.218100
3.23-3.346.70.14223280.0590.1541.294100
3.34-3.466.70.12222820.050.1321.464100
3.46-3.66.60.09723170.040.1061.563100
3.6-3.766.60.08623260.0350.0931.621100
3.76-3.966.60.07523320.030.0811.755100
3.96-4.216.60.06923380.0280.0741.872100
4.21-4.536.50.06323180.0260.0681.919100
4.53-4.996.40.06523460.0270.072.083100
4.99-5.716.40.07123440.030.0772.689100
5.71-7.196.20.07223890.030.0783.78999.9
7.19-505.90.05123600.0220.0555.06395.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→46.93 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 17.288 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2344 5.1 %RANDOM
Rwork0.1958 ---
all0.1986 43986 --
obs0.1986 43986 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.42 Å2 / Biso mean: 81.603 Å2 / Biso min: 44.19 Å2
Baniso -1Baniso -2Baniso -3
1-8.3 Å20 Å20 Å2
2---39.35 Å2-0 Å2
3---31.05 Å2
Refinement stepCycle: LAST / Resolution: 2.65→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7598 0 70 72 7740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197875
X-RAY DIFFRACTIONr_bond_other_d0.0040.027865
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.98910632
X-RAY DIFFRACTIONr_angle_other_deg0.779318134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825919
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12224.986355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.974151475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7341530
X-RAY DIFFRACTIONr_chiral_restr0.0760.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021765
X-RAY DIFFRACTIONr_mcbond_it4.5526.8173682
X-RAY DIFFRACTIONr_mcbond_other4.5336.8163681
X-RAY DIFFRACTIONr_mcangle_it6.62110.224593
LS refinement shellResolution: 2.653→2.722 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 177 -
Rwork0.273 3155 -
all-3332 -
obs-3332 97.66 %
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)
10.1501-0.06460.13460.252-0.36040.5554-0.0241-0.0136-0.0281-0.0653-0.0347-0.05270.065-0.00040.05880.0862-0.01140.02840.13440.01940.024352.664549.661325.029
20.1845-0.0365-0.230.32110.24310.61970.012-0.0312-0.0325-0.18540.03710.021-0.0369-0.1007-0.04910.1508-0.0861-0.0520.12870.08420.056433.047618.213428.2087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 601
2X-RAY DIFFRACTION2B0 - 601

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