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- PDB-2kvc: Solution structure of the Mycobacterium tuberculosis protein Rv05... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2kvc | ||||||
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Title | Solution structure of the Mycobacterium tuberculosis protein Rv0543c, a member of the DUF3349 superfamily. Seattle Structural Genomics Center for Infectious Disease target MytuD.17112.a | ||||||
![]() | Putative uncharacterized protein | ||||||
![]() | UNKNOWN FUNCTION / tuberculosis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | DUF3349, helical bundle / Protein of unknown function DUF3349 / Protein of unknown function (DUF3349) / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
![]() | Buchko, G.W. / Kim, C.Y. / Terwilliger, T.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c. Authors: Buchko, G.W. / Phan, I. / Myler, P.J. / Terwilliger, T.C. / Kim, C.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 525.2 KB | Display | ![]() |
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PDB format | ![]() | 446.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 338.7 KB | Display | ![]() |
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Full document | ![]() | 429.2 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 40.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 11608.073 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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: 300 / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle 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 1% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS. FROM THIS SET OF 20 STRUCTURES 15 STRUCTURES WITH THE FEWEST/FURTHEST CLOSE CONTACTS WERE SELECTED AND SUBMITTED. | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1118 / NOE intraresidue total count: 364 / NOE long range total count: 241 / NOE medium range total count: 209 / NOE sequential total count: 304 / Hydrogen bond constraints total count: 66 / Protein other angle constraints total count: 132 / Protein phi angle constraints total count: 66 / Protein psi angle constraints total count: 66 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 15 |