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- PDB-2rrn: Solution structure of SecDF periplasmic domain P4 -

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Basic information

Entry
Database: PDB / ID: 2rrn
TitleSolution structure of SecDF periplasmic domain P4
ComponentsProbable SecDF protein-export membrane protein
KeywordsPROTEIN TRANSPORT / SecDF / periplasmic domain
Function / homology
Function and homology information


protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein targeting / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #2040 / : / : / Protein translocase subunit SecDF, P1 domain, N-terminal / Protein-export membrane protein SecF, bacterial / Protein translocase subunit SecD / Protein-export membrane protein SecD/SecF, bacterial / Protein-export membrane protein SecD/SecF/SecDF, conserved site / Protein-export membrane protein SecD/SecF, archaeal and bacterial / Protein export membrane protein ...Alpha-Beta Plaits - #2040 / : / : / Protein translocase subunit SecDF, P1 domain, N-terminal / Protein-export membrane protein SecF, bacterial / Protein translocase subunit SecD / Protein-export membrane protein SecD/SecF, bacterial / Protein-export membrane protein SecD/SecF/SecDF, conserved site / Protein-export membrane protein SecD/SecF, archaeal and bacterial / Protein export membrane protein / SecD/SecF GG Motif / Sterol-sensing domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein translocase subunit SecDF
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / Energy Minimization
Model detailsclosest to the average, model 1
AuthorsTanaka, T. / Tsukazaki, T. / Echizen, Y. / Nureki, O. / Kohno, T.
CitationJournal: Nature / Year: 2011
Title: Structure and function of a membrane component SecDF that enhances protein export
Authors: Tsukazaki, T. / Mori, H. / Echizen, Y. / Ishitani, R. / Fukai, S. / Tanaka, T. / Perederina, A. / Vassylyev, D.G. / Kohno, T. / Maturana, A.D. / Ito, K. / Nureki, O.
History
DepositionJan 30, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable SecDF protein-export membrane protein


Theoretical massNumber of molelcules
Total (without water)10,2921
Polymers10,2921
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 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Probable SecDF protein-export membrane protein / SecDF


Mass: 10291.677 Da / Num. of mol.: 1 / Fragment: periplasmic domain P4, residues 470-559
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKE6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1mM [U-13C; U-15N] P4 domain; 20mM TRIS; 50mM sodium chloride; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMP4 domain-1[U-13C; U-15N]1
20 mMTRIS-21
50 mMsodium chloride-31
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
TOPSPINBruker Biospincollection
SPARKYGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
ProcheckNMRLaskowski and MacArthurstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: Energy Minimization / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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