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Yorodumi- PDB-2myy: Solution structure of an MbtH-like protein from Mycobacterium mar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2myy | ||||||
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Title | Solution structure of an MbtH-like protein from Mycobacterium marinum, Seattle Structural Genomics Center for Infectious Disease target MymaA.01649.c | ||||||
Components | Conserved hypothetical MbtH-like protein | ||||||
Keywords | STRUCTURAL 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 | ||||||
Biological species | Mycobacterium marinum M (bacteria) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | closest to the average, model1 | ||||||
Authors | Buchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2myy.cif.gz | 535.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2myy.ent.gz | 453.9 KB | Display | PDB format |
PDBx/mmJSON format | 2myy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/2myy ftp://data.pdbj.org/pub/pdb/validation_reports/my/2myy | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.12 / pH: 7 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 constraints | NOE constraints total: 824 / Hydrogen bond constraints total count: 30 / Protein phi angle constraints total count: 43 / Protein psi angle constraints total count: 43 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |