- PDB-2lky: Solution structure of MSMEG_1053, the second DUF3349 annotated pr... -
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Open data
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Basic information
Entry
Database: PDB / ID: 2lky
Title
Solution structure of MSMEG_1053, the second DUF3349 annotated protein in the genome of Mycobacterium smegmatis, Seattle Structural Genomics Center for Infectious Disease target MysmA.17112.b
Components
Uncharacterized protein
Keywords
Structural Genomics / Unknown Function / infectious disease / tuberculosis / DUF proteins / SSGCID / Seattle Structural Genomics Center for Infectious Disease
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
Mass: 12433.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / Gene: MSMEG_1063 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0QRC1
Sequence details
THE AUTHORS STATE THAT THE PROTEIN WAS OBTAINED VIA PCR CLONING, AND M5 AND V6 ARE PART OF THE ...THE AUTHORS STATE THAT THE PROTEIN WAS OBTAINED VIA PCR CLONING, AND M5 AND V6 ARE PART OF THE PROTEIN SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-15N HSQC
1
2
1
2D 1H-13C HSQC
1
3
1
3D 1H-13C NOESY aliphatic
1
4
1
3D 1H-13C NOESY aromatic
1
5
1
3D 1H-15N NOESY
1
6
1
3D HN(CA)CB
1
7
1
3DHN(COCA)CB
1
8
1
3D HNCO
1
9
1
3DC(CO)NH
1
10
1
2DHBCBCGCDCDHD
1
11
1
2D (HB)CB(CGCDCE)HE
2
12
2
DEUTERIUMEXCHANGE
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1.0 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 1 mM DTT, 20 mM TRIS, 93% H2O/7% D2O
93% H2O/7% D2O
2
1.0 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 1 mM DTT, 20 mM TRIS, 100% D2O
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 (CNSSOLVE) AFTER ADDING 1% TO THE UPPER BOUNDARY LIMIT OF THE UPPER DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS. STRUCTURES WITH 3 OR MORE CLOSE CONTACTS FOLLOWING WATER REFINEMENT, AS DETERMINED BY PSVS, WERE REMOVED FROM THE ENSEMBLE. IN THE END, 17 OUT OF THE 20 CYANA STRUCTURES REFINED EXPLICITLY WITH WATER WERE INCLUDED IN THE FINAL DEPOSITION.
NMR constraints
NOE constraints total: 1726 / NOE intraresidue total count: 1272 / NOE long range total count: 344 / NOE medium range total count: 413 / NOE sequential total count: 515 / Protein phi angle constraints total count: 71 / Protein psi angle constraints total count: 71
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 17
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