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BMRB: 27192

6L6O

NMR assignment of Rab5a (double deletion mutant) from Leishmania donovani

Authors

Maheshwari, D., Yadav, R., Mukhopadhyay, A., Arora, A.

Assembly

Rab5a

Entity

1. Rab5a (polymer, Thiol state: not present), 175 monomers, 19216.68 Da Detail

MNTHPPQLME ATSAKIVMLG ESGAGKSSIA LRFTRNEFLA NQETTIGAAF LSKTVMIDGR ALKYEIWDTA GLERFRSLAP IYYRGASGAL VVYDITNSES LKKAQTWIKE LRANADPSLI IVLVGNKKDL GSLRQVSFED GQRLAAEEQL AAFYEASAKD NNNVEQVFLD LAAKL

Formula weight

19216.68 Da

Source organism

Leishmania donovani

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.3 %, Completeness: 81.7 %, Completeness (bb): 97.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.7 % (1647 of 2015)	80.8 % (841 of 1041)	81.5 % (640 of 785)	87.8 % (166 of 189)
Backbone	97.0 % (1011 of 1042)	96.6 % (345 of 357)	97.3 % (500 of 514)	97.1 % (166 of 171)
Sidechain	70.0 % (796 of 1137)	72.5 % (496 of 684)	69.0 % (300 of 435)	0.0 % (0 of 18)
Aromatic	0.0 % (0 of 138)	0.0 % (0 of 69)	0.0 % (0 of 67)	0.0 % (0 of 2)
Methyl	86.8 % (191 of 220)	91.8 % (101 of 110)	81.8 % (90 of 110)

1. Rab5a

MNTHPPQLME ATSAKIVMLG ESGAGKSSIA LRFTRNEFLA NQETTIGAAF LSKTVMIDGR ALKYEIWDTA GLERFRSLAP IYYRGASGAL VVYDITNSES LKKAQTWIKE LRANADPSLI IVLVGNKKDL GSLRQVSFED GQRLAAEEQL AAFYEASAKD NNNVEQVFLD LAAKL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N labeled

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	DTT	natural abundance	2 mM
5	GTP	natural abundance	1 mM
6	Magnesium chloride	natural abundance	5 mM
7	Glycerol	natural abundance	3 %
8	Rab5a

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N-13C labeled

#	Name	Isotope labeling	Concentration
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.1 %
12	DTT	natural abundance	2 mM
13	GTP	natural abundance	1 mM
14	Magnesium chloride	natural abundance	5 mM
15	Glycerol	natural abundance	3 %
16	Rab5a

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	nitrogen	null	indirect	0.1013291

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	nitrogen	null	indirect	0.1013291

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	nitrogen	null	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	nitrogen	null	indirect	0.1013291

Referencing offset: 0.37 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5YOZ, Strand ID: A Detail

Release date

2017-07-23

Citation

Structural and Biophysical Characterization of Rab5a from Leishmania Donovani
Maheshwari, D., Yadav, R., Rastogi, R., Jain, A., Tripathi, S., Mukhopadhyay, A., Arora, A.
Biophys. J. (2018), 115, 1217-1230, PubMed 30241678 , DOI 10.1016/j.bpj.2018.08.032 , Abstract

Related entities 1. Rab5a, : 1 : 1 : 298 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 15N labeled

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	50 mM
3	sodium azide	natural abundance	0.1 %
4	DTT	natural abundance	2 mM
5	GTP	natural abundance	1 mM
6	Magnesium chloride	natural abundance	5 mM
7	Glycerol	natural abundance	3 %
8	Rab5a

2 3D CBCA(CO)NH