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- PDB-2rpb: The solution structure of membrane protein -

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Basic information

Entry
Database: PDB / ID: 2rpb
TitleThe solution structure of membrane protein
Componentshypothetical membrane protein
KeywordsMEMBRANE PROTEIN / SPFH domain
Function / homology
Function and homology information


Band 7 domain / : / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Tetrahydropterin Synthase; Chain A / Band 7/SPFH domain superfamily ...Band 7 domain / : / Band 7/stomatin-like, conserved site / Band 7 protein family signature. / Stomatin/HflK/HflC family / Band 7 domain / SPFH domain / Band 7 family / prohibitin homologues / Tetrahydropterin Synthase; Chain A / Band 7/SPFH domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
298aa long hypothetical membrane protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics, rigid body restrained molecular dynamics
AuthorsKuwahara, Y. / Unzai, S. / Nagata, T. / Hiroaki, H.
CitationJournal: To be Published
Title: The solution structure of membrane protein
Authors: Kuwahara, Y. / Unzai, S. / Nagata, T. / Hiroaki, H.
History
DepositionMay 13, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical membrane protein


Theoretical massNumber of molelcules
Total (without water)12,8691
Polymers12,8691
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)20 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein hypothetical membrane protein


Mass: 12868.731 Da / Num. of mol.: 1 / Fragment: UNP residues 66-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0470 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codonplus(DE3)-RIL / References: UniProt: O58205

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCANH
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1713D CC(CO)NH
1813D HCC(CO)NH
1923D (H)CCH-TOCSY
11023D 13C-editted NOESY
11113D 15N-editted NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM [U-100% 13C; U-100% 15N] stomatin archea homolog, 20mM HEPES, 90% H2O/10% D2O90% H2O/10% D2O
20.8mM [U-100% 13C] stomatin archea homolog, 20mM HEPES, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMstomatin archea homolog[U-100% 13C; U-100% 15N]1
20 mMHEPES1
0.8 mMstomatin archea homolog[U-100% 13C]2
20 mMHEPES2
Sample conditionsIonic strength: 0 / pH: 7.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.0.17Guntert, Mumenthaler and Wuthrichrefinement
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOL2K.2Koradi, Billeter and Wuthrichrefinement
MOLMOL2K.2Koradi, Billeter and Wuthrichdata analysis
Sparky3.106Goddardchemical shift assignment
Sparky3.106Goddardrefinement
XwinNMR3.5Bruker Biospincollection
RefinementMethod: distance geometry, torsion angle dynamics, rigid body restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 9

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