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- PDB-4lya: EssC (ATPases 2 and 3) from Geobacillus thermodenitrificans (SeMet) -

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Basic information

Entry
Database: PDB / ID: 4lya
TitleEssC (ATPases 2 and 3) from Geobacillus thermodenitrificans (SeMet)
ComponentsUncharacterized protein
KeywordsCELL CYCLE / ESX Secretion / EssC / Type VII Secretion
Function / homology
Function and homology information


ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane
Similarity search - Function
Firmicutes EssC, N-terminal / Firmicutes EssC, C-terminal / DNA transporter / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase ...Firmicutes EssC, N-terminal / Firmicutes EssC, C-terminal / DNA transporter / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ESX secretion system protein EccC
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsDovala, D.L. / Bendebury, A. / Cox, J.S. / Stroud, R.M. / Rosenberg, O.S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2015
Title: Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion.
Authors: Rosenberg, O.S. / Dovala, D. / Li, X. / Connolly, L. / Bendebury, A. / Finer-Moore, J. / Holton, J. / Cheng, Y. / Stroud, R.M. / Cox, J.S.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Structure summary
Revision 1.2Sep 21, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5334
Polymers64,4941
Non-polymers1,0393
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.346, 62.971, 83.888
Angle α, β, γ (deg.)90.00, 107.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 64494.363 Da / Num. of mol.: 1 / Fragment: UNP residues 921-1479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Strain: NG80-2 / Gene: GTNG_0419 / Production host: Escherichia coli (E. coli) / References: UniProt: A4IKE7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG300, 0.1M Na Acetate, pH 4.6, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2012
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 18846 / % possible obs: 97.41 %
Reflection shellResolution: 2.4→2.44 Å / % possible all: 93.79

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Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.45→49.93 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2634 -Random
Rwork0.2084 --
obs-18846 -
Refinement stepCycle: LAST / Resolution: 2.45→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 63 86 4293

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