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- PDB-4zua: Crystal structure of the ExsA regulatory domain -

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Basic information

Entry
Database: PDB / ID: 4zua
TitleCrystal structure of the ExsA regulatory domain
ComponentsExoenzyme S synthesis regulatory protein ExsA
KeywordsTRANSCRIPTION / ExsA / type three secretion / transcription factor / AraC
Function / homology
Function and homology information


positive regulation of DNA-templated transcription initiation / DNA-binding transcription activator activity / negative regulation of protein secretion / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription
Similarity search - Function
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 / RmlC-like jelly roll fold / Homeobox-like domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator ExsA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSchubot, F.D.
CitationJournal: Plos One / Year: 2015
Title: Structural Analysis of the Regulatory Domain of ExsA, a Key Transcriptional Regulator of the Type Three Secretion System in Pseudomonas aeruginosa.
Authors: Shrestha, M. / Xiao, Y. / Robinson, H. / Schubot, F.D.
History
DepositionMay 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exoenzyme S synthesis regulatory protein ExsA
B: Exoenzyme S synthesis regulatory protein ExsA


Theoretical massNumber of molelcules
Total (without water)39,8992
Polymers39,8992
Non-polymers00
Water19811
1
A: Exoenzyme S synthesis regulatory protein ExsA

A: Exoenzyme S synthesis regulatory protein ExsA


Theoretical massNumber of molelcules
Total (without water)39,8992
Polymers39,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2120 Å2
ΔGint-22 kcal/mol
Surface area15170 Å2
MethodPISA
2
B: Exoenzyme S synthesis regulatory protein ExsA

B: Exoenzyme S synthesis regulatory protein ExsA


Theoretical massNumber of molelcules
Total (without water)39,8992
Polymers39,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1370 Å2
ΔGint-17 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.949, 69.949, 191.802
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 Exoenzyme S synthesis regulatory protein ExsA


Mass: 19949.344 Da / Num. of mol.: 2 / Fragment: UNP residues 2-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: exsA, PA1713 / Production host: Escherichia coli (E. coli) / References: UniProt: P26993
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6M MgSO4, 0.1M MES pH 6.5 and 0.1M EGTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2012
RadiationMonochromator: Se / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→56.21 Å / Num. obs: 17161 / % possible obs: 99 % / Redundancy: 20 % / Rmerge(I) obs: 0.86 / Net I/σ(I): 91

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
PHENIXphasing
RefinementResolution: 2.5→56 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 826 4.83 %random
Rwork0.2392 ---
obs0.2406 17118 99.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 0 11 2401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012445
X-RAY DIFFRACTIONf_angle_d1.133319
X-RAY DIFFRACTIONf_dihedral_angle_d18.784899
X-RAY DIFFRACTIONf_chiral_restr0.045386
X-RAY DIFFRACTIONf_plane_restr0.007419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65680.40731300.38412551X-RAY DIFFRACTION96
2.6568-2.86190.39271340.36342653X-RAY DIFFRACTION100
2.8619-3.14990.36091370.28772698X-RAY DIFFRACTION100
3.1499-3.60560.31331410.2652706X-RAY DIFFRACTION99
3.6056-4.54240.22381530.21312739X-RAY DIFFRACTION100
4.5424-560.21931310.19612945X-RAY DIFFRACTION99

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