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- PDB-2myy: Solution structure of an MbtH-like protein from Mycobacterium mar... -

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Basic information

Entry
Database: PDB / ID: 2myy
TitleSolution structure of an MbtH-like protein from Mycobacterium marinum, Seattle Structural Genomics Center for Infectious Disease target MymaA.01649.c
ComponentsConserved hypothetical MbtH-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / infectious diseases / tuberculosis / siderophore assembly / mycobactin / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


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
Conserved hypothetical MbtH-like protein
Similarity search - Component
Biological speciesMycobacterium marinum M (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 an MbtH-like protein from Mycobacterium marinum, Seattle Structural Genomics Center for Infectious Disease target MymaA.01649.c
Authors: Buchko, G.W. / Hewitt, S.N. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionFeb 2, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 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: Conserved hypothetical MbtH-like protein


Theoretical massNumber of molelcules
Total (without water)9,0121
Polymers9,0121
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 Conserved hypothetical MbtH-like protein


Mass: 9011.968 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: BAA-535 / Gene: B2HHJ4, MMAR_3265 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: B2HHJ4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY aliphatic
1213D 1H-13C NOESY aromatic
1313D 1H-15N NOESY
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1712D 1H-15N HSQC
182D2O exchange
191(HB)CB(CGCD)HD
11012D 1H-13C HSQC aliphatic
11112D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O93% H2O/7% D2O
21 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-99% 13C; U-99% 15N]1
100 mMsodium chloride-21
20 mMTRIS-31
1 mMDTT-41
1 mMentity-5[U-99% 13C; U-99% 15N]2
100 mMsodium chloride-62
20 mMTRIS-72
1 mMDTT-82
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 VNMRSAgilentVNMRS8001
Agilent VNMRSAgilentVNMRS6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.115Goddarddata analysis
Sparky3.115Goddardpeak picking
Felix2007Accelrys Software Inc.processing
TALOS+Cornilescu, Delaglio and Baxdata 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: 824 / Hydrogen bond constraints total count: 30 / Protein phi angle constraints total count: 43 / Protein psi angle constraints total count: 43
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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