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- PDB-2lra: NMR Structure of Signal Sequence Deleted (SSD) Rv0603 Protein fro... -

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Basic information

Entry
Database: PDB / ID: 2lra
TitleNMR Structure of Signal Sequence Deleted (SSD) Rv0603 Protein from Mycobacterium tuberculosis without N-terminal His-tag
ComponentsPOSSIBLE EXPORTED PROTEIN
KeywordsIMMUNE SYSTEM / SSD
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 / water refinement
Model detailslowest energy, model 1
AuthorsTripathi, S. / Pulavarti, S. / Yadav, R. / Jain, A. / Pathak, P. / Meher, A. / Arora, A.
CitationJournal: To be Published
Title: NMR Structure of Signal Sequence Deleted (SSD) Rv0603 Protein from Mycobacterium tuberculosis without N-terminal His-tag
Authors: Tripathi, S. / Pulavarti, S. / Yadav, R. / Jain, A. / Pathak, P. / Meher, A. / Arora, A.
History
DepositionMar 28, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2May 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: POSSIBLE EXPORTED PROTEIN


Theoretical massNumber of molelcules
Total (without water)8,2361
Polymers8,2361
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein POSSIBLE EXPORTED PROTEIN / Rv0603-SSD


Mass: 8235.750 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 28-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / 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
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D HNCO
1523D HN(CO)CA
1623D H(CCO)NH
1723D C(CO)NH
1823D (H)CCH-TOCSY
1932D 1H-13C HSQC aliphatic
11032D 1H-13C HSQC aromatic
11122D CB(CGCD)HD
11222D CB(CGCE)HE
11322D 1H-1H NOESY aromatic
11413D 1H-15N NOESY
11533D 1H-13C NOESY aliphatic
11633D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate-1, 50 mM sodium chloride-2, 0.1 % sodium azide-3, 1 mM AEBSF protease inhibitor-4, 1 mM [U-99% 15N] Rv0603-SSD-5, 93% H2O/7% D2O93% H2O/7% D2O
220 mM sodium phosphate-6, 50 mM sodium chloride-7, 0.1 % sodium azide-8, 1 mM AEBSF protease inhibitor-9, 1 mM [U-99% 13C; U-99% 15N] Rv0603-SSD-10, 93% H2O/7% D2O93% H2O/7% D2O
320 mM sodium phosphate-11, 50 mM sodium chloride-12, 0.1 % sodium azide-13, 1 mM AEBSF protease inhibitor-14, 1 mM [U-99% 13C; U-99% 15N] Rv0603-SSD-15, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate-11
50 mMsodium chloride-21
0.1 %sodium azide-31
1 mMAEBSF protease inhibitor-41
1 mMRv0603-SSD-5[U-99% 15N]1
20 mMsodium phosphate-62
50 mMsodium chloride-72
0.1 %sodium azide-82
1 mMAEBSF protease inhibitor-92
1 mMRv0603-SSD-10[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate-113
50 mMsodium chloride-123
0.1 %sodium azide-133
1 mMAEBSF protease inhibitor-143
1 mMRv0603-SSD-15[U-99% 13C; U-99% 15N]3
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
Cyana3.0Guntert, Mumenthaler and Wuthrichstructure solution
PSVS1.4Bhattacharya and Montelionevalidation of structure quality
CNSsolve_1.21refinement
RefinementMethod: water refinement / Software ordinal: 1
NMR constraintsNOE constraints total: 1235 / NOE intraresidue total count: 319 / NOE long range total count: 391 / NOE medium range total count: 190 / NOE sequential total count: 335 / Protein chi angle constraints total count: 4 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 61
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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