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- PDB-3fd9: Crystal Structure of the transcriptional anti-activator ExsD from... -

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Basic information

Entry
Database: PDB / ID: 3fd9
TitleCrystal Structure of the transcriptional anti-activator ExsD from Pseudomonas aeruginosa
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Anti-activator / Transcription regulation / Pseudomonas / repressor / type III secretion
Function / homology
Function and homology information


ExsD N-terminal domain-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #190 / Antiactivator protein ExsD / Antiactivator protein ExsD, domain 1 / Antiactivator protein ExsD, domain 2 / Antiactivator protein ExsD N-terminal domain / ESAT-6-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Helicase, Ruva Protein; domain 3 / Helix Hairpins ...ExsD N-terminal domain-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #190 / Antiactivator protein ExsD / Antiactivator protein ExsD, domain 1 / Antiactivator protein ExsD, domain 2 / Antiactivator protein ExsD N-terminal domain / ESAT-6-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Helicase, Ruva Protein; domain 3 / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsSchubot, F.D.
CitationJournal: Protein Sci. / Year: 2009
Title: Structural evidence suggests that antiactivator ExsD from Pseudomonas aeruginosa is a DNA binding protein
Authors: Bernhards, R.C. / Jing, X. / Vogelaar, N.J. / Robinson, H. / Schubot, F.D.
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)87,3233
Polymers87,3233
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-26 kcal/mol
Surface area35420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.755, 69.347, 86.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein


Mass: 29107.633 Da / Num. of mol.: 3 / Fragment: residues 22-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Strain: PA01 / Gene: exsD, PA14_42380 / Plasmid: pDestHMBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q02KK5, UniProt: A0A0H2Z989*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 277 K / pH: 6.8
Details: 0.1 M Bis-Tris (pH 6.8), 0.2 M Ammonium Acetate, and 30% polyethylene glycol 3350 was combined at a 1:1 ratio with 20ExsD solution at 15 mg/ml in 25 mM Tris-HCl (pH 7.4), 0.15 M NaCl, 2 mM ...Details: 0.1 M Bis-Tris (pH 6.8), 0.2 M Ammonium Acetate, and 30% polyethylene glycol 3350 was combined at a 1:1 ratio with 20ExsD solution at 15 mg/ml in 25 mM Tris-HCl (pH 7.4), 0.15 M NaCl, 2 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→29.401 Å / Num. obs: 23616 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.39 / % possible all: 57.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.4 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1 / Phase error: 26.59 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.263 1213 5.14 %
Rwork0.213 --
obs0.215 23613 86.4 %
all-23613 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.76 Å2 / ksol: 0.27 e/Å3
Displacement parametersBiso mean: 50.17 Å2
Baniso -1Baniso -2Baniso -3
1--6.4078 Å2-0 Å20 Å2
2---10.5746 Å2-0 Å2
3---9.0783 Å2
Refine analyzeLuzzati coordinate error obs: 0.357 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5754 0 0 119 5873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055877
X-RAY DIFFRACTIONf_angle_d0.8327982
X-RAY DIFFRACTIONf_dihedral_angle_d17.2492165
X-RAY DIFFRACTIONf_chiral_restr0.058862
X-RAY DIFFRACTIONf_plane_restr0.0031039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70710.3172670.26271335X-RAY DIFFRACTION47
2.7071-2.83020.3237900.26841944X-RAY DIFFRACTION68
2.8302-2.97930.33091300.26282322X-RAY DIFFRACTION81
2.9793-3.16580.30641360.2532620X-RAY DIFFRACTION92
3.1658-3.40990.25971470.22832713X-RAY DIFFRACTION96
3.4099-3.75240.26731580.20372783X-RAY DIFFRACTION97
3.7524-4.29390.23571810.18392805X-RAY DIFFRACTION98
4.2939-5.40440.21681540.17022861X-RAY DIFFRACTION98
5.4044-29.40290.24561500.19223017X-RAY DIFFRACTION98
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)
11.38810.45140.21651.27060.27271.15520.0673-0.05170.23860.21420.0307-0.02160.11630.0134-0.10780.21310.03890.01930.19010.03690.23431.101939.889560.4792
21.57-1.03560.08911.70880.31921.2531-0.2158-0.0998-0.21890.38260.12910.0025-0.01680.17370.05140.3340.0661-0.02530.31920.08880.143745.470616.640769.8123
30.472-0.10820.25611.6416-0.51881.0342-0.0701-0.1666-0.02510.18890.13630.0079-0.0099-0.0933-0.05930.1460.0168-0.02290.21040.00320.196257.742234.774550.9032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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