BMRBj - BMREntryMaster

Found 1 Document (0.691 seconds)

BMRB: 25685

2N4X

Structure of the Transmembrane Electron Transporter CcdA

Authors

Chou, J.J., Williamson, J.A.

Assembly

Transmembrane Electron Transporter CcdA

Entity

1. Transmembrane Electron Transporter CcdA (polymer, Thiol state: not present), 208 monomers, 22754.03 Da Detail

GSTSQEQPTA QLMAFALGIL SVFSPAVLPV VPLIFAGSRG RALDAFLIVA GLTISMLILG YTASLFFGFF RVVAMLFLLI FALILLSDEL DEKVSIFASR MTSGLSWKIQ TLPSFFFGML LAFLWLPAIL PFAGIAISQT LLSENPLVML SYGLGMAVTI AAVFKMGEKF VKANFQLIRK VTGAIVLLYL AYFALTEVLL LEHHHHHH

Formula weight

22754.03 Da

Source organism

Archaeoglobus fulgidus

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 85.6 %, Completeness: 38.4 %, Completeness (bb): 69.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	38.4 % (955 of 2490)	22.3 % (281 of 1260)	49.7 % (507 of 1020)	79.5 % (167 of 210)
Backbone	69.0 % (850 of 1232)	49.1 % (207 of 422)	78.2 % (477 of 610)	83.0 % (166 of 200)
Sidechain	17.0 % (247 of 1452)	9.1 % (76 of 838)	28.1 % (170 of 604)	10.0 % (1 of 10)
Aromatic	3.6 % (10 of 280)	1.4 % (2 of 140)	5.8 % (8 of 138)	0.0 % (0 of 2)
Methyl	17.5 % (59 of 338)	13.6 % (23 of 169)	21.3 % (36 of 169)

1. CcdA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6 (±0.1), Details The sample contains ~100 mM Foscholine-12 (DPC) as membrane mimetic for the membrane protein

#	Name	Isotope labeling	Concentration
1	CcdA	[U-100% 13C; U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	50 (±1.0) mM
4	dodecylphosphocholine	natural abundance	100 (±10.0) mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6 (±0.1), Details The sample contains ~100 mM Foscholine-12 (DPC) as membrane mimetic for the membrane protein

#	Name	Isotope labeling	Concentration
7	CcdA	[U-100% 13C; U-100% 15N]	0.8 (±0.2) mM
8	MES	natural abundance	20 (±1.0) mM
9	sodium chloride	natural abundance	50 (±1.0) mM
10	dodecylphosphocholine	[U-99% 2H]	100 (±10.0) mM
11	H2O	natural abundance	95 (±10.0) %
12	D2O	natural abundance	5 (±10.0) %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	na	methyl carbon	na	indirect	0.2514495
¹H	TMS	methyl protons	external	direct	1.0
¹⁵N	na	nitrogen	na	indirect	0.1013291

Referencing offset: -0.3 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	na	methyl carbon	na	indirect	0.2514495
¹H	TMS	methyl protons	external	direct	1.0
¹⁵N	na	nitrogen	na	indirect	0.1013291

Referencing offset: -0.3 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	na	methyl carbon	na	indirect	0.2514495
¹H	TMS	methyl protons	external	direct	1.0
¹⁵N	na	nitrogen	na	indirect	0.1013291

Referencing offset: -0.26 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2N4X, Strand ID: A Detail

Release date

2015-09-01

Citation

Structure and multistate function of the transmembrane electron transporter CcdA
Williamson, J.A., Cho, S., Ye, J., Collet, J., Beckwith, J.R., Chou, J.J.
Nat. Struct. Mol. Biol. (2015), 22, 809-814, PubMed 26389738 , DOI 10.1038/nsmb.3099 , Abstract

Related entities 1. Transmembrane Electron Transporter CcdA, : 4 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N TROSY-HSQC

Instrument

Bruker Avance - 600 MHz Used for collecting triple resonance spectra

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6 (±0.1), Details The sample contains ~100 mM Foscholine-12 (DPC) as membrane mimetic for the membrane protein

#	Name	Isotope labeling	Concentration
1	CcdA	[U-100% 13C; U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	50 (±1.0) mM
4	dodecylphosphocholine	natural abundance	100 (±10.0) mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

2 3D TROSY HNCA

Instrument

Bruker Avance - 600 MHz Used for collecting triple resonance spectra

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-100% 13C; U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	50 (±1.0) mM
4	dodecylphosphocholine	natural abundance	100 (±10.0) mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

3 3D TROSY HN(CO)CA

Instrument

Bruker Avance - 600 MHz Used for collecting triple resonance spectra

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-100% 13C; U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	50 (±1.0) mM
4	dodecylphosphocholine	natural abundance	100 (±10.0) mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

4 3D TROSY HN(CA)CO

Instrument

Bruker Avance - 600 MHz Used for collecting triple resonance spectra

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-100% 13C; U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	50 (±1.0) mM
4	dodecylphosphocholine	natural abundance	100 (±10.0) mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

5 3D TROSY HNCO

Instrument

Bruker Avance - 600 MHz Used for collecting triple resonance spectra

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-100% 13C; U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	50 (±1.0) mM
4	dodecylphosphocholine	natural abundance	100 (±10.0) mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

6 3D TROSY HNCACB

Instrument

Bruker Avance - 600 MHz Used for collecting triple resonance spectra

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-100% 13C; U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	50 (±1.0) mM
4	dodecylphosphocholine	natural abundance	100 (±10.0) mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

7 2D 1H-15N TROSY-HSQC

Instrument

Bruker Avance - 800 MHz Used for collecting NOE spectra

Sample

#	Name	Isotope labeling	Concentration
7	CcdA	[U-100% 13C; U-100% 15N]	0.8 (±0.2) mM
8	MES	natural abundance	20 (±1.0) mM
9	sodium chloride	natural abundance	50 (±1.0) mM
10	dodecylphosphocholine	[U-99% 2H]	100 (±10.0) mM
11	H2O	natural abundance	95 (±10.0) %
12	D2O	natural abundance	5 (±10.0) %

8 3D 15N-edited NOESY TROSY-HSQC (60 ms mix time)

Instrument

Bruker Avance - 800 MHz Used for collecting NOE spectra

Sample

#	Name	Isotope labeling	Concentration
7	CcdA	[U-100% 13C; U-100% 15N]	0.8 (±0.2) mM
8	MES	natural abundance	20 (±1.0) mM
9	sodium chloride	natural abundance	50 (±1.0) mM
10	dodecylphosphocholine	[U-99% 2H]	100 (±10.0) mM
11	H2O	natural abundance	95 (±10.0) %
12	D2O	natural abundance	5 (±10.0) %

9 3D 15N-edited NOESY TROSY-HSQC (120 ms mix time)

Instrument

Bruker Avance - 800 MHz Used for collecting NOE spectra

Sample

#	Name	Isotope labeling	Concentration
7	CcdA	[U-100% 13C; U-100% 15N]	0.8 (±0.2) mM
8	MES	natural abundance	20 (±1.0) mM
9	sodium chloride	natural abundance	50 (±1.0) mM
10	dodecylphosphocholine	[U-99% 2H]	100 (±10.0) mM
11	H2O	natural abundance	95 (±10.0) %
12	D2O	natural abundance	5 (±10.0) %

10 3D 13C-edited Methyl NOESY (150 ms mix time)

Instrument

Bruker Avance - 800 MHz Used for collecting NOE spectra

Sample

#	Name	Isotope labeling	Concentration
7	CcdA	[U-100% 13C; U-100% 15N]	0.8 (±0.2) mM
8	MES	natural abundance	20 (±1.0) mM
9	sodium chloride	natural abundance	50 (±1.0) mM
10	dodecylphosphocholine	[U-99% 2H]	100 (±10.0) mM
11	H2O	natural abundance	95 (±10.0) %
12	D2O	natural abundance	5 (±10.0) %

11 4D double 15N-edited NOESY (200 ms mix time)

Instrument

Bruker Avance - 600 MHz Used for collecting triple resonance spectra

Sample

#	Name	Isotope labeling	Concentration
1	CcdA	[U-100% 13C; U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	50 (±1.0) mM
4	dodecylphosphocholine	natural abundance	100 (±10.0) mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25685_2n4x.nef
Input source #2: Coordindates	2n4x.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

------------------10--------20--------30--------40--------50--------60--------70--------80--------90
GSTSQEQPTAQLMAFALGILSVFSPAVLPVVPLIFAGSRGRALDAFLIVAGLTISMLILGYTASLFFGFFRVVAMLFLLIFALILLSDELDEKVSIFASR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSTSQEQPTAQLMAFALGILSVFSPAVLPVVPLIFAGSRGRALDAFLIVAGLTISMLILGYTASLFFGFFRVVAMLFLLIFALILLSDELDEKVSIFASR
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190
MTSGLSWKIQTLPSFFFGMLLAFLWLPAILPFAGIAISQTLLSENPLVMLSYGLGMAVTIAAVFKMGEKFVKANFQLIRKVTGAIVLLYLAYFALTEVLL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MTSGLSWKIQTLPSFFFGMLLAFLWLPAILPFAGIAISQTLLSENPLVMLSYGLGMAVTIAAVFKMGEKFVKANFQLIRKVTGAIVLLYLAYFALTEVLL
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

--------
LEHHHHHH
||||||||
LEHHHHHH
--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	208	0	0	100.0

Content subtype: combined_25685_2n4x.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_CcdA_reduced	Warning	765		80.3 (chain: A, length: 208)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	680 (1)	noe	75.0 (chain: A, length: 208)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	238 (238)	.	64.9 (chain: A, length: 208)

Assigned chemical shifts

Saveframe: chem_shift_CcdA_reduced
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 80.3%
- Total number of assignments
  - ¹H chemical shifts: 158
  - ¹³C chemical shifts: 451
  - ¹⁵N chemical shifts: 156
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1260	158	12.5
¹³C chemical shifts	1020	451	44.2
¹⁵N chemical shifts	215	156	72.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	422	158	37.4
¹³C chemical shifts	416	320	76.9
¹⁵N chemical shifts	200	156	78.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	838	0	0.0
¹³C chemical shifts	604	131	21.7
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	177	0	0.0
¹³C chemical shifts	177	20	11.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	140	0	0.0
¹³C chemical shifts	138	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 75.0%
- Total number of restraints: 680
- Weight of restraints: 1.0 (680)
- Potential type of restraints: square-well-parabolic (680)
- Range of distance target values: 1.25, 5.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 64.9%
- Total number of restraints: 238
- Total number of restraints per polymer type: 238
- Weight of restraints: 1.0 (238)
- Potential type of restraints: square-well-parabolic (238)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ccda, dsbd homolog, transmembrane electron transporter, transmembrane reductase

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Found 1 Document (0.691 seconds)

BMRB: 25685

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Transmembrane Electron Transporter CcdA, : 4 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 4 contents Detail