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- PDB-2k3m: Rv1761c -

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Basic information

Entry
Database: PDB / ID: 2k3m
TitleRv1761c
ComponentsRv1761c
KeywordsMEMBRANE PROTEIN / PROTEIN / integral membrane protein
Function / homologyProtein of unknown function DUF5073 / Domain of unknown function (DUF5073) / membrane / Chem-MTN / Possible exported protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsintegral membrane protein
AuthorsPage, R.C. / Moore, J.D. / Lee, S. / Opella, S.J. / Cross, T.A.
CitationJournal: Protein Sci. / Year: 2009
Title: Backbone structure of a small helical integral membrane protein: A unique structural characterization.
Authors: Page, R.C. / Lee, S. / Moore, J.D. / Opella, S.J. / Cross, T.A.
History
DepositionMay 14, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 20, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rv1761c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0294
Polymers16,2351
Non-polymers7933
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Rv1761c


Mass: 16235.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv
Description: ligation independent cloning vector producing N-terminal His6 tag
Gene: MT1810, Rv1761c / Plasmid: pTBSG1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06796
#2: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL


Mass: 264.385 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18NO3S2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: integral membrane protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1142D 1H-15N HSQC
1212D 1H-15N HSQC
1322D 1H-15N HSQC
1432D 1H-15N HSQC
1543D HNCO
1643D HNCA
1743D HN(CA)CB
1843D HN(CO)CA
1943D CBCA(CO)NH
11052D 1H-15N HSQC
11152D 1H-15N HSQC
11253D 1H-15N NOESY
11362D 1H-15N HSQC-IPAP
11472D 1H-15N HSQC-IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 15N] Rv1761c, 0.4 mM CYSP, 10 % D2O, 90 % H2O, 20 mM sodium acetate, 150 mM DPC, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-100% 15N] Rv1761c, 0.4 mM CYSP, 10 % D2O, 90 % H2O, 20 mM sodium acetate, 150 mM DPC, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-100% 15N] Rv1761c, 0.4 mM CYSP, 10 % D2O, 90 % H2O, 20 mM sodium acetate, 150 mM DPC, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] Rv1761c, 10 % D2O, 90 % H2O, 20 mM sodium acetate, 150 mM DPC, 90% H2O/10% D2O90% H2O/10% D2O
51 mM [U-100% 15N] Rv1761c, 10 % D2O, 90 % H2O, 20 mM sodium acetate, 150 mM DPC, 90% H2O/10% D2O90% H2O/10% D2O
61 mM [U-100% 15N] Rv1761c, 10 % D2O, 90 % H2O, 20 mM sodium acetate, 150 mM DPC, 5 % polyacrylamide gel, 90% H2O/10% D2O90% H2O/10% D2O
71 mM [U-100% 15N] Rv1761c, 10 % D2O, 90 % H2O, 20 mM sodium acetate, 150 mM DPC, 4.4 % polyacrylamide gel, 1.1 % 2-acrylamido-2-methyl-1-propanesulfonic acid, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMRv1761c[U-100% 15N]1
0.4 mMCYSP1
10 %D2O1
90 %H2O1
20 mMsodium acetate1
150 mMDPC1
0.4 mMRv1761c[U-100% 15N]2
0.4 mMCYSP2
10 %D2O2
90 %H2O2
20 mMsodium acetate2
150 mMDPC2
0.4 mMRv1761c[U-100% 15N]3
0.4 mMCYSP3
10 %D2O3
90 %H2O3
20 mMsodium acetate3
150 mMDPC3
1 mMRv1761c[U-100% 13C; U-100% 15N]4
10 %D2O4
90 %H2O4
20 mMsodium acetate4
150 mMDPC4
1 mMRv1761c[U-100% 15N]5
10 %D2O5
90 %H2O5
20 mMsodium acetate5
150 mMDPC5
1 mMRv1761c[U-100% 15N]6
10 %D2O6
90 %H2O6
20 mMsodium acetate6
150 mMDPC6
5 %polyacrylamide gel6
1 mMRv1761c[U-100% 15N]7
10 %D2O7
90 %H2O7
20 mMsodium acetate7
150 mMDPC7
4.4 %polyacrylamide gel7
1.1 %2-acrylamido-2-methyl-1-propanesulfonic acid7
Sample conditionsIonic strength: 170 / pH: 4 / Pressure: ambient / Temperature: 323 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7203
Varian AvanceVarianAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
VNMRVarianchemical shift assignment
XwinNMRBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 105 / Protein psi angle constraints total count: 105
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

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