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- PDB-2iut: P. aeruginosa FtsK motor domain, dimeric -

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Basic information

Entry
Database: PDB / ID: 2iut
TitleP. aeruginosa FtsK motor domain, dimeric
ComponentsDNA TRANSLOCASE FTSK
KeywordsMEMBRANE PROTEIN / NUCLEOTIDE-BINDING / CHROMOSOME PARTITION / ATP-BINDING / DNA- BINDING / CELL DIVISION / DNA TRANSLOCATION / KOPS / MEMBRANE / DIVISOME / CELL CYCLE
Function / homology
Function and homology information


cellular response to antibiotic / chromosome segregation / cell division / DNA binding / ATP binding / plasma membrane
Similarity search - Function
Threonyl-tRNA Synthetase; Chain A, domain 2 - #40 / FtsK gamma domain / DNA translocase FtsK, 4TM region / FtsK alpha domain / Ftsk gamma domain / 4TM region of DNA translocase FtsK/SpoIIIE / FtsK alpha domain / Ftsk_gamma / Threonyl-tRNA Synthetase; Chain A, domain 2 / FtsK domain ...Threonyl-tRNA Synthetase; Chain A, domain 2 - #40 / FtsK gamma domain / DNA translocase FtsK, 4TM region / FtsK alpha domain / Ftsk gamma domain / 4TM region of DNA translocase FtsK/SpoIIIE / FtsK alpha domain / Ftsk_gamma / Threonyl-tRNA Synthetase; Chain A, domain 2 / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA translocase FtsK
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMassey, T.H. / Mercogliano, C.P. / Yates, J. / Sherratt, D.J. / Lowe, J.
CitationJournal: Mol.Cell / Year: 2006
Title: Double-Stranded DNA Translocation: Structure and Mechanism of Hexameric Ftsk
Authors: Massey, T.H. / Mercogliano, C.P. / Yates, J. / Sherratt, D.J. / Lowe, J.
History
DepositionJun 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA TRANSLOCASE FTSK
B: DNA TRANSLOCASE FTSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5476
Polymers125,4522
Non-polymers1,0954
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.168, 57.431, 98.057
Angle α, β, γ (deg.)94.57, 93.80, 107.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA TRANSLOCASE FTSK / FTSK MOTOR DOMAIN


Mass: 62726.141 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 247-811
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9I0M3
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDNA MOTOR PROTEIN, WHICH IS BOTH REQUIRED TO MOVE DNA OUT OF THE REGION OF THE SEPTUM DURING CELL ...DNA MOTOR PROTEIN, WHICH IS BOTH REQUIRED TO MOVE DNA OUT OF THE REGION OF THE SEPTUM DURING CELL DIVISION AND FOR THE SEPTUM FORMATION. TRACKS DNA IN AN ATP-DEPENDENT MANNER BY GENERATING POSITIVE SUPERCOILS IN FRONT OF IT AND NEGATIVE SUPERCOILS BEHIND IT (BY SIMILARITY).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.25→100 Å / Num. obs: 39962 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.1
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / % possible all: 93.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→100 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 2106 5 %RANDOM
Rwork0.2207 ---
obs0.2207 42413 93.8 %-
Solvent computationBsol: 47.2759 Å2 / ksol: 0.362925 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1--1.652 Å25.779 Å21.995 Å2
2---4.05 Å24.55 Å2
3---5.702 Å2
Refinement stepCycle: LAST / Resolution: 2.25→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6244 0 64 365 6673
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.422
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.27 Å / Rfactor Rfree: 0.3893 / Rfactor Rwork: 0.3819 / Total num. of bins used: 42
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ATG.PARAM

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