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- PDB-2eww: Crystal Structure of the Pilus Retraction Motor PilT and Bound ATP -

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Basic information

Entry
Database: PDB / ID: 2eww
TitleCrystal Structure of the Pilus Retraction Motor PilT and Bound ATP
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'-TRIPHOSPHATE / : / Twitching motility protein PilT
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 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: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: twitching motility protein PilT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0672
Polymers42,5591
Non-polymers5071
Water362
1
A: twitching motility protein PilT
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)258,39912
Polymers255,3566
Non-polymers3,0436
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)107.380, 107.380, 68.860
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: 42559.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: GenBank: 15606134, UniProt: O66950*PLUS
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.31 %
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 ATP , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-ID-B10.9794
SYNCHROTRONAPS 14-ID-B20.9568
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2003
RadiationMonochromator: Diamond / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.95681
ReflectionResolution: 3.2→20 Å / Num. obs: 7481 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1093 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→19.47 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.838 / SU B: 29.41 / SU ML: 0.499 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.642 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30981 395 5.4 %RANDOM
Rwork0.23868 ---
all0.2423 7481 --
obs0.24236 6948 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 70.716 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.26 Å20 Å2
2---0.52 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 31 2 2750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222796
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.9993782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5315341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91624.065123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.00515521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.661521
X-RAY DIFFRACTIONr_chiral_restr0.0660.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022051
X-RAY DIFFRACTIONr_nbd_refined0.2070.21284
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.25
X-RAY DIFFRACTIONr_mcbond_it0.3531.51754
X-RAY DIFFRACTIONr_mcangle_it0.64122770
X-RAY DIFFRACTIONr_scbond_it0.56931138
X-RAY DIFFRACTIONr_scangle_it1.0194.51012
LS refinement shellResolution: 3.203→3.284 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 24 -
Rwork0.301 479 -
obs--91.45 %

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