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Found 1 Document (1.302 seconds)

BMRB: 19242

2M8C

The solution NMR structure of E. coli apo-HisJ

Authors

Chu, B.C. H., Vogel, H.J.

Assembly

apo-HisJ

Entity

1. apo-HisJ (polymer, Thiol state: all disulfide bound), 241 monomers, 26477.57 Da Detail

GGMAIPQNIR IGTDPTYAPF ESKNSQGELV GFDIDLAKEL CKRINTQCTF VENPLDALIP SLKAKKIDAI MSSLSITEKR QQEIAFTDKL YAADSRLVVA KNSDIQPTVE SLKGKRVGVL QGTTQETFGN EHWAPKGIEI VSYQGQDNIY SDLTAGRIDA AFQDEVAASE GFLKQPVGKD YKFGGPSVKD EKLFGVGTGM GLRKEDNELR EALNKAFAEM RADGTYEKLA KKYFDFDVYG G

Formula weight

26477.57 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS41:SG	1:CYS48:SG

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.6 %, Completeness: 48.8 %, Completeness (bb): 83.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	48.8 % (1357 of 2781)	27.3 % (396 of 1450)	67.7 % (729 of 1077)	91.3 % (232 of 254)
Backbone	83.8 % (1197 of 1428)	54.4 % (270 of 496)	99.6 % (697 of 700)	99.1 % (230 of 232)
Sidechain	24.1 % (379 of 1571)	13.3 % (127 of 954)	42.0 % (250 of 595)	9.1 % (2 of 22)
Aromatic	3.5 % (7 of 200)	4.0 % (4 of 100)	3.0 % (3 of 99)	0.0 % (0 of 1)
Methyl	20.6 % (52 of 252)	15.1 % (19 of 126)	26.2 % (33 of 126)

1. apo-HisJ

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
1	apo-HisJ	[U-13C; U-15N; U-2H]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %
5	DSS	natural abundance	0.5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
6	apo-HisJ	[U-13C; U-15N]	1 mM
7	sodium phosphate	natural abundance	50 mM
8	D2O	natural abundance	10 %
9	H2O	natural abundance	90 %
10	DSS	natural abundance	0.5 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Concentration
11	apo-HisJ	[U-13C; U-15N]	1 mM
12	sodium phosphate	natural abundance	50 mM
13	D2O	natural abundance	100 %
14	DSS	natural abundance	0.5 mM

Protein Blocks Logo

Calculated from 30 models in PDB: 2M8C, Strand ID: A Detail

Release date

2013-09-29

Citation

Role of the two structural domains from the periplasmic Escherichia coli histidine-binding protein HisJ
Chu, B.C.H., Dewolf, T., Vogel, H.J.
J. Biol. Chem. (2013), 288, 31409-31422, PubMed 24036119 , DOI 10.1074/jbc.M113.490441 , Abstract

Related entities 1. apo-HisJ, : 1 : 2 : 166 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_19242_2m8c.nef
Input source #2: Coordindates	2m8c.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

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:41:CYS:SG	A:48:CYS:SG	oxidized, CA 62.39, CB 46.86 ppm	oxidized, CA 53.17, CB 47.29 ppm	2.018

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-------100
GGMAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGMAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVA

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

-------210-------220-------230-------240-
GLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG
|||||||||||||||||||||||||||||||||||||||||
GLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	241	0	0	100.0

Content subtype: combined_19242_2m8c.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1155		99.6 (chain: A, length: 241)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1370 (1)	noe	93.4 (chain: A, length: 241)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	74 (1)	hbond	25.7 (chain: A, length: 241)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	407 (407)	.	97.5 (chain: A, length: 241)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	185 (185)	.	76.8 (chain: A, length: 241)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 241, Sequence coverage: 99.6%
- Total number of assignments
  - ¹³C chemical shifts: 697
  - ¹H chemical shifts: 229
  - ¹⁵N chemical shifts: 229
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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 (%)
¹³C chemical shifts	1077	697	64.7
¹H chemical shifts	1450	229	15.8
¹⁵N chemical shifts	263	229	87.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	482	480	99.6
¹H chemical shifts	496	229	46.2
¹⁵N chemical shifts	232	229	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	595	217	36.5
¹H chemical shifts	954	0	0.0
¹⁵N chemical shifts	31	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	130	21	16.2
¹H chemical shifts	130	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	99	0	0.0
¹H chemical shifts	100	0	0.0
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 241, Sequence coverage: 93.4%
- Total number of restraints: 1370
- Weight of restraints: 1.0 (1370)
- Potential type of restraints: square-well-parabolic (1370)
- Range of distance target values: 2.9, 5.15 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 241, Sequence coverage: 25.7%
  - Total number of restraints: 74
  - Weight of restraints: 1.0 (74)
  - Potential type of restraints: square-well-parabolic (74)
  - Range of distance target values: 1.0, 1.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 241, Sequence coverage: 97.5%
- Total number of restraints: 407
- Total number of restraints per polymer type: 407
- Weight of restraints: 1.0 (407)
- Potential type of restraints: square-well-parabolic (407)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 241, Sequence coverage: 76.8%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GGMAIPQNIRIGTDPTYAPFESKNSQGELVGFDIDLAKELCKRINTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVA
         ||| | ||| ||||      |||||||||||||||||||||||| ||||| || || |||||| ||||||| |||||||||||   |||||
.........RIG.D.TYA.FESK......VGFDIDLAKELCKRINTQCTFVEN.LDALI.SL.AK.IDAIMS.LSITEKR.QEIAFTDKLYA...RLVVA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
KNSDIQPTVESLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEGFLKQPVGKDYKFGGPSVKDEKLFGVGTGM
| ||   |||||||||||| |||||||||||||| |||||| ||  |||||||||| ||||||||||||||  ||  || || || |||||      |||
K.SD...TVESLKGKRVGV.QGTTQETFGNEHWA.KGIEIV.YQ..DNIYSDLTAG.IDAAFQDEVAASEG..KQ..GK.YK.GG.SVKDE......TGM
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

-------210-------220-------230-------240-
GLRKEDNELREALNKAFAEMRADGTYEKLAKKYFDFDVYGG
||||||||||||| |||||||||||||||||||   |||  
GLRKEDNELREAL.KAFAEMRADGTYEKLAKKY...DVY  
-------210-------220-------230---------

Total number of restraints: 185
Potential type of restraints: undefined (185)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords apo, E. coli, HisJ, Periplasmic binding protein

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Found 1 Document (1.302 seconds)

BMRB: 19242

Sample #1

Sample #2

Sample #3

Related entities 1. apo-HisJ, : 1 : 2 : 166 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail