BMRBj - BMREntryMaster

Found 1 Document (3.527 seconds)

BMRB: 18493

2LTQ

High resolution structure of DsbB C41S by joint calculation with solid-state NMR and X-ray data

Authors

Tang, M., Sperling, L.J., Schwieters, C.D., Nesbitt, A.E., Gennis, R.B., Rienstra, C.M.

Assembly

DsbB C41S

Entity

1. DsbB (polymer, Thiol state: free and disulfide bound), 176 monomers, 20089.81 × 2 Da Detail

MLRFLNQASQ GRGAWLLMAF TALALELTAL WFQHVMLLKP SVLCIYERVA LFGVLGAALI GAIAPKTPLR YVAMVIWLYS AFRGVQLTYE HTMLQLYPSP FATCDFMVRF PEWLPLDKWV PQVFVASGDC AERQWDFLGL EMPQWLLGIF IAYLIVAVLV VISQPFKAKK RDLFGR

2. DsbB C41S, entity 2 (polymer), 239 monomers, 26339.16 × 2 Da Detail

MDSQAQVLIL LLLWVSGTCG DIVMSQSPSS LAVSAGEKVT MSCKSSQSLL NSRTRKNYLA WYQQKPGQSP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVQAEDLA VYYCKQSYNL YTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER QNGVLNSWTD QDSKDSTYSM SSTLTLTKDE YERHNSYTCE ATHKTSTSPI VKSFNRNEC

3. DsbB C41S, entity 3 (polymer), 221 monomers, 23646.24 × 2 Da Detail

EVQLVESGGG LVKPGGSLKL SCAASGFAFS SYDMSWVRQT PEKRLEWVAY ISSGGGSTYY PDTVKGRFTI SRDNAKNTLY LQMSSLKSED TAMYYCARPD YRSYAMDYWG QGTSVTVSSA KTTAPSVYPL APVCGDTTGS SVTLGCLVKG YFPEPVTLTW NSGSLSSGVH TFPAVLQSDL YTLSSSVTVT SSTWPSQSIT CNVAHPASST KVDKKIEPRG P

4. DsbB C41S, entity UQ1 (non-polymer), 250.290 × 2 Da

Total weight

140651.0 Da

Max. entity weight

26339.16 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS104:SG	1:CYS130:SG

Source organism

Escherichia coli , Mus musculus

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 25.9 %, Completeness: 12.8 %, Completeness (bb): 17.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	12.8 % (934 of 7318)	6.3 % (235 of 3759)	19.4 % (562 of 2896)	20.7 % (137 of 663)
Backbone	17.7 % (664 of 3750)	10.3 % (132 of 1283)	21.2 % (396 of 1864)	22.6 % (136 of 603)
Sidechain	9.6 % (399 of 4160)	4.2 % (103 of 2476)	18.2 % (295 of 1624)	1.7 % (1 of 60)
Aromatic	5.2 % (37 of 718)	5.6 % (20 of 359)	5.0 % (17 of 342)	0.0 % (0 of 17)
Methyl	18.5 % (133 of 720)	6.9 % (25 of 360)	30.0 % (108 of 360)

1. DsbB

MLRFLNQASQ GRGAWLLMAF TALALELTAL WFQHVMLLKP SVLCIYERVA LFGVLGAALI GAIAPKTPLR YVAMVIWLYS AFRGVQLTYE HTMLQLYPSP FATCDFMVRF PEWLPLDKWV PQVFVASGDC AERQWDFLGL EMPQWLLGIF IAYLIVAVLV VISQPFKAKK RDLFGR

2. entity 2

3. entity 3

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 261 K, pH 7.8

#	Name	Isotope labeling	Concentration
1	DsbB	[U-100% 13C; U-100% 15N]	7 mg
2	DDM	natural abundance	2 mg
3	E. coli lipids	natural abundance	7 mg

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 261 K, pH 7.8

#	Name	Isotope labeling	Concentration
4	DsbB	[2-13C-glycerol; U-15N]	5 mg
5	DDM	natural abundance	2 mg
6	E. coli lipids	natural abundance	7 mg

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 261 K, pH 7.8

#	Name	Isotope labeling	Concentration
7	DsbB	[1,3-13C-glycerol; U-15N]	4 mg
8	DDM	natural abundance	2 mg
9	E. coli lipids	natural abundance	7 mg

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	alkane carbons	40.48 ppm	external	direct	1.0
¹⁵N	DSS	alkane carbons	40.48 ppm	external	indirect	0.4029799

Referencing offset: -0.14 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	alkane carbons	40.48 ppm	external	direct	1.0
¹⁵N	DSS	alkane carbons	40.48 ppm	external	indirect	0.4029799

Referencing offset: -0.14 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	alkane carbons	40.48 ppm	external	direct	1.0
¹⁵N	DSS	alkane carbons	40.48 ppm	external	indirect	0.4029799

Referencing offset: -0.69 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LTQ, Strand ID: A, B, C, D, E, F Detail

Release date

2013-02-26

Citation

Structure of the disulfide bond generating membrane protein DsbB in the lipid bilayer
Tang, M., Nesbitt, A.E., Sperling, L.J., Berthold, D.A., Schwieters, C.D., Gennis, R.B., Rienstra, C.M.
J. Mol. Biol. (2013), 425, 1670-1682, PubMed 23416557 , DOI 10.1016/j.jmb.2013.02.009 , Abstract

Related entities 1. DsbB, : 1 : 1 : 8 : 66 entities Detail

Related entities 2. DsbB C41S, entity 2, : 370 entities Detail

Related entities 3. DsbB C41S, entity 3, : 467 entities Detail

Interaction partners 1. DsbB, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:104:CYS:SG	A:130:CYS:SG	oxidized, CA 64.988, CB 42.988 ppm	oxidized, CA 64.581, CB 42.879 ppm	2.01
B:43:CYS:SG	B:114:CYS:SG	unknown	unknown	2.044
B:159:CYS:SG	B:219:CYS:SG	unknown	unknown	2.039
B:239:CYS:SG	C:134:CYS:SG	unknown	unknown	1.944
C:22:CYS:SG	C:96:CYS:SG	unknown	unknown	2.041
C:146:CYS:SG	C:201:CYS:SG	unknown	unknown	2.04
D:104:CYS:SG	D:130:CYS:SG	unknown	unknown	2.033
E:43:CYS:SG	E:114:CYS:SG	unknown	unknown	2.045
E:159:CYS:SG	E:219:CYS:SG	unknown	unknown	2.053
E:239:CYS:SG	F:134:CYS:SG	unknown	unknown	1.953
F:22:CYS:SG	F:96:CYS:SG	unknown	unknown	2.046
F:146:CYS:SG	F:201:CYS:SG	unknown	unknown	2.031

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
G	1	UQ1	UBIQUINONE-1	Assigned chemical shifts
G	2	UQ1	UBIQUINONE-1	None

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	176	100.0
B	B	239	100.0
C	C	221	100.0
D	D	176	100.0
E	E	239	100.0
F	F	221	100.0

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	12		No information
1	Assigned chemical shifts	assigned_chemical_shifts_list_DsbB	Warning	744		86.4 (chain: A, length: 176), 50.0 (chain: G, length: 2)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	2754 (1)	undefined	69.3 (chain: A, length: 176), 69.3 (chain: D, length: 176)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	372 (372)	.	64.8 (chain: A, length: 176), 64.8 (chain: D, length: 176)

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
12	ARG	CZ	159.227
34	HIS	CG	137.404
65	PRO	N	128.226
68	PRO	N	129.713
70	ARG	CZ	159.739
77	TRP	CG	114.126
91	HIS	CG	136.131
98	PRO	N	130.765
100	PRO	N	130.137
165	PRO	N	134.035

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	875	508	58.1
¹H chemical shifts	1115	67	6.0
¹⁵N chemical shifts	192	120	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	352	246	69.9
¹H chemical shifts	352	67	19.0
¹⁵N chemical shifts	166	120	72.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	523	262	50.1
¹H chemical shifts	763	0	0.0
¹⁵N chemical shifts	26	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	134	103	76.9
¹H chemical shifts	134	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	128	5	3.9
¹H chemical shifts	135	0	0.0
¹⁵N chemical shifts	7	0	0.0

Comp_index_ID	Comp_ID
1	UQ1
2	UQ1

Keywords DsbB C41S, Fab, Joint calculations, Solid-state NMR, X-ray reflections

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18493_2ltq.nef
Input source #2: Coordindates	2ltq.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

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Found 1 Document (3.527 seconds)

BMRB: 18493

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DsbB, : 1 : 1 : 8 : 66 entities Detail

Related entities 2. DsbB C41S, entity 2, : 370 entities Detail

Related entities 3. DsbB C41S, entity 3, : 467 entities Detail

Interaction partners 1. DsbB, : 1 interactors Detail

Experiments performed 5 experiments Detail

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NMR combined restraints 4 contents Detail