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- PDB-2m7g: Structure of the Type IVa Major Pilin from the Electrically Condu... -

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Basic information

Entry
Database: PDB / ID: 2m7g
TitleStructure of the Type IVa Major Pilin from the Electrically Conductive Bacterial Nanowires of Geobacter sulfurreducens
ComponentsGeopilin domain 1 protein
KeywordsCell Adhesion / Structural Protein / Electron Transport / pilin / PilA / bacterial nanowire / type IVa
Function / homology:
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsfewest violations, model 10
AuthorsReardon, P.N. / Mueller, K.T.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of the Type IVa Major Pilin from the Electrically Conductive Bacterial Nanowires of Geobacter sulfurreducens.
Authors: Reardon, P.N. / Mueller, K.T.
History
DepositionApr 22, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geopilin domain 1 protein


Theoretical massNumber of molelcules
Total (without water)6,5771
Polymers6,5771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Geopilin domain 1 protein


Mass: 6576.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: DL-1 / KN400 / Gene: KN400_1523, pila, pilA-N / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: D7AIT1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D HNCO
1313D HNCA
1413D CBCA(CO)NH
1513D HNHA
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] PilA, 200 mM [U-2H] DHPC, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPilA-1[U-13C; U-15N]1
200 mMDHPC-2[U-2H]1
Sample conditionspH: 5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRsVarianVNMRs8001
Varian VNMRsVarianVNMRs7502

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ3.2Variancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CARAKeller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 755 / NOE intraresidue total count: 172 / NOE long range total count: 1 / NOE medium range total count: 329 / NOE sequential total count: 253
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 18 / Maximum upper distance constraint violation: 0.47 Å

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