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- PDB-2eyu: The Crystal Structure of the C-terminal Domain of Aquifex aeolicu... -

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Basic information

Entry
Database: PDB / ID: 2eyu
TitleThe Crystal Structure of the C-terminal Domain of Aquifex aeolicus PilT
Componentstwitching motility protein PilT
KeywordsPROTEIN TRANSPORT / Pilus Retraction Motor / C-terminal Domain PilT
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Pilus retraction protein PilT/PilU / : / Type II/IV secretion system protein / Type II/IV secretion system protein / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Twitching motility protein PilT
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.87 Å
AuthorsSatyshur, K.A. / Worzalla, G.A. / Meyer, L.S. / Heiniger, E.K. / Aukema, K.G. / 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 9, 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 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
B: twitching motility protein PilT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8423
Polymers59,7462
Non-polymers961
Water30617
1
A: twitching motility protein PilT


Theoretical massNumber of molelcules
Total (without water)29,8731
Polymers29,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: twitching motility protein PilT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9692
Polymers29,8731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.150, 89.150, 70.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein twitching motility protein PilT


Mass: 29873.084 Da / Num. of mol.: 2 / Fragment: PilT C-terminal Domain / Mutation: Glu294Gly
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / References: GenBank: 15606134, UniProt: O66950*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.17 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mg/ml protein 0.1 M Mes 10% Dioxane 1.6 M ammonium sulfate , pH 6.5, 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: 0.97934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.86→40 Å / Num. all: 45173 / Num. obs: 44351 / % possible obs: 96.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 49.9
Reflection shellResolution: 1.86→1.94 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 7.8 / % possible all: 83.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.87→20 Å / Num. parameters: 15692 / Num. restraintsaints: 16007 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
Details: Crystal is twinned, with BASF refined to 0.535 in ShelX h,-k,-l
RfactorNum. reflection% reflectionSelection details
Rwork0.17 ---
all0.1746 42952 --
obs-42952 98.18 %-
Rfree---RANDOM
Displacement parametersBiso mean: 35.3 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3922
Refinement stepCycle: LAST / Resolution: 1.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 5 17 3920
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0288
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.111
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.87→1.871 Å /
Rfactor% reflection
Rwork0.208 -
obs-82.8 %

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