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- PDB-2khr: Solution structure of Rv2377c, a MbtH-like protein from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 2khr
TitleSolution structure of Rv2377c, a MbtH-like protein from Mycobacterium tuberculosis
ComponentsProtein mbtH
KeywordsBIOSYNTHETIC PROTEIN / siderophores / mycobactin / MtbH-like / 2-hydroxyphenyloxazoline / tuberculosis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


siderophore biosynthetic process / cytosol
Similarity search - Function
Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein MbtH / Protein MbtH
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsBuchko, G.W. / Kim, C.Y. / Terwilliger, T.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2010
Title: Solution structure of Rv2377c-founding member of the MbtH-like protein family.
Authors: Buchko, G.W. / Kim, C.Y. / Terwilliger, T.C. / Myler, P.J.
History
DepositionApr 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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: Protein mbtH


Theoretical massNumber of molelcules
Total (without water)8,3721
Polymers8,3721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein mbtH


Mass: 8372.165 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mbtH, MT2445.1, MTCY27.03, Rv2377c / Plasmid: modifed pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21PRO / References: UniProt: O05821, UniProt: P9WIP5*PLUS

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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
1313D 1H-13C NOESY
1413D 1H-15N TOCSY
1513D HN(CA)CB
1613D HNCO
1713D HN(COCA)CB
1813D C(CO)NH
1913D (H)CCH-TOCSY
11012D 1H-13C HSQC
11113D H(CCO)NH
1122deuterium X-change

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-98% 13C; U-98% 15N] Rv2377c, 300 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-98% 13C; U-98% 15N] Rv2377c, 300 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMRv2377c-1[U-98% 13C; U-98% 15N]1
300 mMsodium chloride-21
20 mMTRIS-31
1 mMDTT-41
2 mMRv2377c-5[U-98% 13C; U-98% 15N]2
300 mMsodium chloride-62
20 mMTRIS-72
1 mMDTT-82
Sample conditionsIonic strength: 0.32 / pH: 7.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA9002
Varian INOVAVarianINOVA6003
Varian UnityPlusVarianUNITYPLUS5004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Felix2007Accelrys Software Inc.processing
Sparky3.115Goddardchemical shift assignment
Sparky3.115Goddardpeak picking
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESYASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESYASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY REMARK IN EXPLICIT WATER (CNS) AFTER ADDING 10% TO THE UPPER BOUNDARY LIMIT. THE FINAL SET OF STRUCTURES CONTAINED NO DIHEDRAL VIOLATIONS GREATER THAN 2 DEGREE OR DISTANCE VIOLATIONS TOTAL THAT WERE GREATER THAN 0.05 ANGSTROM.
NMR constraintsNOE constraints total: 602 / NOE intraresidue total count: 142 / NOE long range total count: 187 / NOE medium range total count: 77 / NOE sequential total count: 196
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.05 Å / Maximum upper distance constraint violation: 0.05 Å

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