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- PDB-2n6g: Solution structure of an MbtH-like protein from Mycobacterium avi... -

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Basic information

Entry
Database: PDB / ID: 2n6g
TitleSolution structure of an MbtH-like protein from Mycobacterium avium, Seattle Structural Genomics Center for Infectious Disease target MyavA.01649.c
ComponentsMbtH-like protein
KeywordsUNKNOWN FUNCTION / SSGCID / tuberculosis / infectious diseases / mbtH-like / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyMbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / siderophore biosynthetic process / cytosol / Conserved domain protein
Function and homology information
Biological speciesMycobacterium avium 104 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model1
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Solution structure of a MbtH-like protein from Mycobacterium avium.
Authors: Buchko, G.W. / Hewitt, S.N. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 20, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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 / _pdbx_nmr_software.name
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: MbtH-like protein


Theoretical massNumber of molelcules
Total (without water)8,9951
Polymers8,9951
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 #1closest to the average

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Components

#1: Protein MbtH-like protein


Mass: 8994.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium 104 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0H2ZVT0*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
1212D 1H-13C HSQC aliphatic
1313D HNCO
1413D C(CO)NH
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11013D H(CCO)NH
1111deuterium exchange
NMR detailsText: The sample was not very stable and multiple samples were made (same conditions) to collect the data.

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Sample preparation

DetailsContents: 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMsodium chloride-11
20 mMTRIS-21
1 mMDTT-31
Sample conditionsIonic strength: 0.12 / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent INOVAAgilentINOVA6001
Agilent INOVAAgilentINOVA5002
Agilent VNMRSAgilentVNMRS7503
Agilent VNMRSAgilentVNMRS8004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Felix2007Accelrys Software Inc.processing
Sparky3.115Goddarddata analysis
Sparky3.115Goddardpeak picking
PSVS1.5Bhattacharya and Montelionedata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). 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 NOESY ASSIGNMENTS). 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 MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS.
NMR constraintsNOE constraints total: 357 / Protein phi angle constraints total count: 36 / Protein psi angle constraints total count: 36
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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