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- PDB-2ewv: Crystal Structure of the Pilus Retraction Motor PilT and Bound ADP -

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Basic information

Entry
Database: PDB / ID: 2ewv
TitleCrystal Structure of the Pilus Retraction Motor PilT and Bound ADP
Componentstwitching motility protein PilT
KeywordsPROTEIN TRANSPORT / Pilus Retraction Motor / ATPase / Hexameric PilT
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / : / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold ...Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / : / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Twitching motility protein PilT
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSatyshur, K.A. / Forest, K.T.
Citation
Journal: Structure / Year: 2007
Title: Crystal structures of the pilus retraction motor PilT suggest large domain movements and subunit cooperation drive motility.
Authors: Satyshur, K.A. / Worzalla, G.A. / Meyer, L.S. / Heiniger, E.K. / Aukema, K.G. / Misic, A.M. / Forest, K.T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: The pilus-retraction protein PilT: ultrastructure of the biological assembly
Authors: Forest, K.T. / Satyshur, K.A. / Worzalla, G.A. / Hansen, J.K. / Herdendorf, T.J.
History
DepositionNov 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: twitching motility protein PilT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5182
Polymers42,0901
Non-polymers4271
Water34219
1
A: twitching motility protein PilT
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)255,10612
Polymers252,5436
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Unit cell
Length a, b, c (Å)108.240, 108.240, 69.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by all six operations in P6.

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Components

#1: Protein twitching motility protein PilT


Mass: 42090.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: GenBank: 15606134, UniProt: O66950*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 5-8 mg/ml protein 30-45% MPD 0.2-0.4 M Ammonium Sulfate Tris, 15mM KCl 75mM 5% glycerol 5-10mM magnesium Chloride 1-5 mM ATPgammaS , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2003
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 15167 / Num. obs: 12021 / % possible obs: 79.25 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rsym value: 0.063
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.52 / Num. unique all: 625 / Rsym value: 0.317 / % possible all: 78.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
TWIN_LSQrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PilT-ATP

Resolution: 2.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2669 546 Random
Rwork0.1856 --
all-11469 -
obs-11092 -
Displacement parametersBiso mean: 78.35 Å2
Baniso -1Baniso -2Baniso -3
1-26.641 Å26.103 Å20 Å2
2--26.641 Å20 Å2
3----53.281 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 27 19 2763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008415
X-RAY DIFFRACTIONc_angle_deg1.51396
X-RAY DIFFRACTIONc_dihedral_angle_d24.39212
X-RAY DIFFRACTIONc_improper_angle_d0.89598
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.3833 63 -
Rwork0.3744 --
obs-1093 78.9 %

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