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- PDB-5fl3: PilT2 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5fl3
TitlePilT2 from Thermus thermophilus
ComponentsPILI RETRACTION PROTEIN PILT
KeywordsTRANSPORT PROTEIN / ATPASE
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / Bacterial type II secretion system protein E signature. / : / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / Bacterial type II secretion system protein E signature. / : / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Pili retraction protein PilT
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsKaruppiah, V. / Derrick, J.P.
CitationJournal: To be Published
Title: Pilt2 from Thermus Thermophilus
Authors: Karuppiah, V. / Derrick, J.P.
History
DepositionOct 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: PILI RETRACTION PROTEIN PILT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7494
Polymers41,1951
Non-polymers5553
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.750, 106.750, 71.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PILI RETRACTION PROTEIN PILT / PILT2


Mass: 41194.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5SHF6
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.85 Å3/Da / Density % sol: 56.9 % / Description: NONE
Crystal growDetails: 0.1M BIS-TRIS/HCL PH 5.5, 1%(W/V) PEG 3350, 1.0 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.52→42.76 Å / Num. obs: 15793 / % possible obs: 99.9 % / Observed criterion σ(I): 2.4 / Redundancy: 6.8 % / Biso Wilson estimate: 44.26 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.9
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EWV

2ewv


Resolution: 2.52→42.761 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 779 4.9 %
Rwork0.1853 --
obs0.1883 15770 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→42.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 34 45 2867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092870
X-RAY DIFFRACTIONf_angle_d1.2793887
X-RAY DIFFRACTIONf_dihedral_angle_d15.9041097
X-RAY DIFFRACTIONf_chiral_restr0.046455
X-RAY DIFFRACTIONf_plane_restr0.006493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5202-2.6780.34651440.25272478X-RAY DIFFRACTION100
2.678-2.88480.33621210.23912492X-RAY DIFFRACTION100
2.8848-3.1750.30791200.23092467X-RAY DIFFRACTION100
3.175-3.63420.29011250.21022511X-RAY DIFFRACTION100
3.6342-4.57790.23041280.15312510X-RAY DIFFRACTION100
4.5779-42.76710.17721410.15172533X-RAY DIFFRACTION100

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