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- PDB-4mlo: 1.65A resolution structure of ToxT from Vibrio cholerae (P21 Form) -

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Basic information

Entry
Database: PDB / ID: 4mlo
Title1.65A resolution structure of ToxT from Vibrio cholerae (P21 Form)
ComponentsTCP pilus virulence regulatory protein
KeywordsTRANSCRIPTION REGULATOR / ToxT / DNA Binding
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
ToxT, HTH1 motif / Jelly Rolls - #810 / ToxT, HTH1 motif superfamily / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein ...ToxT, HTH1 motif / Jelly Rolls - #810 / ToxT, HTH1 motif superfamily / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PALMITOLEIC ACID / Pilus/toxin transcriptional regulator ToxT
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLovell, S. / Wehmeyer, G. / Battaile, K.P. / Li, J. / Egan, S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: 1.65 angstrom resolution structure of the AraC-family transcriptional activator ToxT from Vibrio cholerae.
Authors: Li, J. / Wehmeyer, G. / Lovell, S. / Battaile, K.P. / Egan, S.M.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TCP pilus virulence regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4535
Polymers32,0921
Non-polymers3614
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.337, 39.410, 80.238
Angle α, β, γ (deg.)90.000, 97.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TCP pilus virulence regulatory protein


Mass: 32092.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: toxT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BGC0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 5% (w/V) PEG 5000, 10% (v/v) 2-propanol, 0.1 M MES, 0.2M magnesium chloride, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→79.47 Å / Num. all: 35493 / Num. obs: 35493 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 16.89 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1753 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA0.1.29data scaling
PHASER2.5.5phasing
PHENIXdev_1444refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBG

3gbg


Resolution: 1.65→39.735 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 1777 5.01 %RANDOM
Rwork0.1678 ---
obs0.1692 35477 99.51 %-
all-35477 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.54 Å2 / Biso mean: 25.9375 Å2 / Biso min: 4.03 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 21 179 2333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092247
X-RAY DIFFRACTIONf_angle_d0.9473043
X-RAY DIFFRACTIONf_chiral_restr0.046349
X-RAY DIFFRACTIONf_plane_restr0.006379
X-RAY DIFFRACTIONf_dihedral_angle_d11.89837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69460.26711260.228225732699100
1.6946-1.74450.27861280.22782591271999
1.7445-1.80080.26811460.22062541268799
1.8008-1.86510.25511410.21192564270599
1.8651-1.93980.27981320.20362533266599
1.9398-2.02810.22791260.18525852711100
2.0281-2.1350.20021260.152526242750100
2.135-2.26880.19731380.150725832721100
2.2688-2.44390.19871220.149626162738100
2.4439-2.68980.15581250.153426082733100
2.6898-3.07890.1771680.162925892757100
3.0789-3.87860.17581370.158626232760100
3.8786-39.74630.17141620.15972670283299
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)
10.39530.27290.07820.3878-0.05550.2155-0.0304-0.3843-0.12250.07420.0487-0.0258-0.0583-0.47660.04090.11260.05330.03480.38520.00470.0576-17.3045-7.3897-20.2983
20.12220.03070.02650.04670.05640.1503-0.0928-0.18380.03020.1352-0.0197-0.0104-0.1049-0.1808-0.00190.28140.0439-0.02690.2865-0.00560.1552-5.6738-3.7903-8.0266
30.205-0.0608-0.04930.1943-0.10570.2029-0.0458-0.05720.0074-0.00770.0438-0.03420.011-0.03510.00820.06330.0019-0.00370.0172-0.00010.067-3.8737-8.7481-33.5627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 87 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 159 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 272 )A0

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