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- PDB-2muy: The solution structure of the FtsH periplasmic N-domain -

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Basic information

Entry
Database: PDB / ID: 2muy
TitleThe solution structure of the FtsH periplasmic N-domain
ComponentsATP-dependent zinc metalloprotease FtsH
KeywordsNUCLEOTIDE BINDING PROTEIN / AAA ATPase / substrate recognition domain / metalloprotease
Function / homologySignal recognition particle alu RNA binding heterodimer, srp9/1 - #210 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, NOESY back-calculation
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsScharfenberg, F. / Serek-Heuberger, J. / Martin, J. / Lupas, A.N. / Coles, M.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure and Evolution of N-domains in AAA Metalloproteases.
Authors: Scharfenberg, F. / Serek-Heuberger, J. / Coles, M. / Hartmann, M.D. / Habeck, M. / Martin, J. / Lupas, A.N. / Alva, V.
History
DepositionSep 18, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent zinc metalloprotease FtsH


Theoretical massNumber of molelcules
Total (without water)9,5461
Polymers9,5461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein ATP-dependent zinc metalloprotease FtsH / FtsH-N


Mass: 9545.575 Da / Num. of mol.: 1 / Fragment: N-domain (UNP residues 25-96)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsH, ECMDS42_2646 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: H0QE60

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D CBCA(CO)NH
1223D HN(CA)CB
1323D HNCO
1423D HN(CA)CO
1523D C(CO)NH
1623D (H)CCH-TOCSY
1723D CCH NOESY
1823D CNH NOESY
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11113D HNHA
11213D HNHB

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 15N] FtsH-N, 15 mM sodium phosphate, 75 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [U-100% 13C; U-100% 15N] FtsH-N, 15 mM sodium phosphate, 75 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMFtsH-N-1[U-100% 15N]1
15 mMsodium phosphate-21
75 mMsodium chloride-31
0.7 mMFtsH-N-4[U-100% 13C; U-100% 15N]2
15 mMsodium phosphate-52
75 mMsodium chloride-62
Sample conditionsIonic strength: 0.105 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker DMXBrukerDMX7502
Bruker AvanceBrukerAvance9003

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Processing

NMR software
NameVersionDeveloperClassification
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
SPARKYGoddardchemical shift assignment
SPARKYGoddarddata analysis
X-PLOR_NIH2.9.4Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIH2.9.4Schwieters, Kuszewski, Tjandra and Clorerefinement
NMR-SPIRIT1.1In houserefinement
RefinementMethod: simulated annealing, NOESY back-calculation / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 41 / Protein other angle constraints total count: 13 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 63
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.07 Å / Maximum torsion angle constraint violation: 0.6 ° / Maximum upper distance constraint violation: 0.09 Å
NMR ensemble rmsDistance rms dev: 0.011 Å / Distance rms dev error: 0.001 Å

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