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- PDB-2ius: E. coli FtsK motor domain -

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Basic information

Entry
Database: PDB / ID: 2ius
TitleE. coli FtsK motor domain
ComponentsDNA TRANSLOCASE FTSK
KeywordsMEMBRANE PROTEIN / NUCLEOTIDE-BINDING / CHROMOSOME PARTITION / ATP-BINDING / DNA-BINDING / CELL DIVISION / TRANSMEMBRANE / INNER MEMBRANE / HEXAMERIC RING / DNA TRANSLOCATION / KOPS / MEMBRANE / DIVISOME / CELL CYCLE / AAA ATPASE
Function / homology
Function and homology information


double-stranded DNA helicase activity / divisome complex / septum digestion after cytokinesis / DNA translocase activity / division septum assembly / FtsZ-dependent cytokinesis / response to osmotic stress / cellular response to antibiotic / cell division site / response to salt stress ...double-stranded DNA helicase activity / divisome complex / septum digestion after cytokinesis / DNA translocase activity / division septum assembly / FtsZ-dependent cytokinesis / response to osmotic stress / cellular response to antibiotic / cell division site / response to salt stress / chromosome segregation / sequence-specific DNA binding / cell division / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / membrane / 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 / : ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA translocase FtsK
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
C: DNA TRANSLOCASE FTSK
D: DNA TRANSLOCASE FTSK
E: DNA TRANSLOCASE FTSK
F: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)337,6006
Polymers337,6006
Non-polymers00
Water9,962553
1
A: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)56,2671
Polymers56,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)56,2671
Polymers56,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)56,2671
Polymers56,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)56,2671
Polymers56,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)56,2671
Polymers56,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: DNA TRANSLOCASE FTSK


Theoretical massNumber of molelcules
Total (without water)56,2671
Polymers56,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.600, 117.200, 132.800
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA TRANSLOCASE FTSK / FTSK MOTOR DOMAIN


Mass: 56266.695 Da / Num. of mol.: 6 / Fragment: MOTOR DOMAIN, RESIDUES 818-1329 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P46889
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 997 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 997 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LYS 997 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 997 TO ALA ENGINEERED RESIDUE IN CHAIN C, LYS 997 TO ALA ENGINEERED RESIDUE IN CHAIN D, LYS 997 TO ALA ENGINEERED RESIDUE IN CHAIN E, LYS 997 TO ALA ENGINEERED RESIDUE IN CHAIN F, LYS 997 TO ALA 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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 51 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 80156 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→100 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 4082 5 %RANDOM
Rwork0.2459 ---
obs0.2459 80677 99.8 %-
Solvent computationBsol: 47.0167 Å2 / ksol: 0.350993 e/Å3
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1--3.791 Å20 Å2-2.002 Å2
2--5.579 Å20 Å2
3----1.788 Å2
Refinement stepCycle: LAST / Resolution: 2.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18016 0 0 553 18569
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_deg1.405
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: 2.7→2.72 Å / Rfactor Rfree: 0.3746 / Rfactor Rwork: 0.3097 / Total num. of bins used: 50
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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