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BMRB: 30153

5SXY

The solution NMR structure for the PqqD truncation of Methylobacterium extorquens PqqCD representing a functional and stand-alone ribosomally synthesized and post-translational modified (RiPP) recognition element (RRE)

Authors

Evans, R.L., Xia, Y., Wilmot, C.M.

Assembly

Bifunctional coenzyme PQQ synthesis protein C/D (E.C.1.3.3.11)

Entity

1. Bifunctional coenzyme PQQ synthesis protein C/D (E.C.1.3.3.11) (polymer, Thiol state: not present), 94 monomers, 10408.84 Da Detail

MEPTAFSGSD VPRLPRGVRL RFDEVRNKHV LLAPERTFDL DDNAVAVLKL VDGRNTVSQI AQILGQTYDA DPAIIEADIL PMLAGLAQKR VLER

Formula weight

10408.84 Da

Source organism

Methylorubrum extorquens AM1

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.1 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.1 % (994 of 1079)	90.6 % (508 of 561)	94.1 % (398 of 423)	92.6 % (88 of 95)
Backbone	97.1 % (536 of 552)	96.3 % (180 of 187)	97.1 % (269 of 277)	98.9 % (87 of 88)
Sidechain	88.5 % (545 of 616)	87.7 % (328 of 374)	91.9 % (216 of 235)	14.3 % (1 of 7)
Aromatic	71.4 % (30 of 42)	81.0 % (17 of 21)	61.9 % (13 of 21)
Methyl	92.4 % (122 of 132)	92.4 % (61 of 66)	92.4 % (61 of 66)

1. entity 1

MEPTAFSGSD VPRLPRGVRL RFDEVRNKHV LLAPERTFDL DDNAVAVLKL VDGRNTVSQI AQILGQTYDA DPAIIEADIL PMLAGLAQKR VLER

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 4.6 mg/mL [U-13C; U-15N] PqqD, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	PqqD	[U-13C; U-15N]		4.6 mg/mL
2	potassium phosphate	natural abundance		25 mM

LACS Plot; CA

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

Referencing offset: 0.01 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.01 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.08 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5SXY, Strand ID: A Detail

Release date

2016-11-22

Citation

(1)H, (13)C, and (15)N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA
Evans, R.L., Latham, J.A., Klinman, J.P., Xia, Y., Wilmot, C.M., Evans, R.L., Latham, J.A., Klinman, J.P., Wilmot, C.M., Xia, Y.
Biomol. NMR Assign. (2016), 10, 385-389, PubMed 27638737 , DOI 10.1007/s12104-016-9705-8 , Abstract

Related entities 1. Bifunctional coenzyme PQQ synthesis protein C/D (E.C.1.3.3.11), : 1 : 1 : 36 entities Detail

Experiments performed 16 experiments Detail

1 3D HNCACB