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- PDB-2kgy: Solution structure of Rv0603 protein from Mycobacterium tuberculo... -

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Basic information

Entry
Database: PDB / ID: 2kgy
TitleSolution structure of Rv0603 protein from Mycobacterium tuberculosis H37Rv
ComponentsPOSSIBLE EXPORTED PROTEIN
KeywordsIMMUNE SYSTEM / Rv0603 / Secretory protein
Function / homologySHC Adaptor Protein - #20 / SHC Adaptor Protein / 2-Layer Sandwich / Alpha Beta / Possible exported protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsTripathi, S. / Pulavarti, S.V.S.R.K. / Pathak, P.P. / Meher, A.K. / Jain, A. / Arora, A.
CitationJournal: To be Published
Title: Solution structure of Rv0603 protein from Mycobacterium tuberculosis H37Rv
Authors: Tripathi, S. / Pulavarti, S.V.S.R.K. / Pathak, P.P. / Meher, A.K. / Jain, A. / Arora, A.
History
DepositionMar 23, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: 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: POSSIBLE EXPORTED PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,0101
Polymers11,0101
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein POSSIBLE EXPORTED PROTEIN / Rv0603 protein


Mass: 11009.763 Da / Num. of mol.: 1 / Fragment: UNP residues 28-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0603 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21(DE3) / References: UniProt: O07775

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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 1H-15N NOESY
1323D HNCA
1423D HN(CA)CB
1523D CBCA(CO)NH
1623D HNCO
1723D HN(CO)CA
1823D (H)CCH-TOCSY
1922D 1H-13C HSQC aliphatic
11023D 1H-13C NOESY aliphatic
11122D 1H-13C HSQC aromatic
11223D 1H-13C NOESY aromatic
11323D H(CCCO)NH-TOCSY
1142D (H)CCC(O)NH-TOCSY
11522D CB(CGCD)HD
11622D CB(CGCE)HE

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Sample preparation

Details
Solution-IDContentsSolvent system
120mM sodium phosphate-1, 50mM sodium chloride-2, 0.1% sodium azide-3, 1mM [U-99% 15N] Rv0603-SSD-4, 1mM AEBSF-5, 95% H2O/5% D2O95% H2O/5% D2O
220mM sodium phosphate-6, 50mM sodium chloride-7, 0.1% sodium azide-8, 1mM [U-99% 13C; U-99% 15N] Rv0603-SSD-9, 1mM AEBSF-10, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate-11
50 mMsodium chloride-21
0.1 %sodium azide-31
1 mMRv0603-SSD-4[U-99% 15N]1
1 mMAEBSF-51
20 mMsodium phosphate-62
50 mMsodium chloride-72
0.1 %sodium azide-82
1 mMRv0603-SSD-9[U-99% 13C; U-99% 15N]2
1 mMAEBSF-102
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
CARAKeller and Wuthrichdata analysis
XEASYBartels et al.data analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichsolution structure representation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 912 / NOE intraresidue total count: 324 / NOE long range total count: 201 / NOE medium range total count: 139 / NOE sequential total count: 296 / Protein phi angle constraints total count: 86 / Protein psi angle constraints total count: 86
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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