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BMRB: 17509

2LA7

NMR structure of the protein YP_557733.1 from Burkholderia xenovorans

Authors

Jaudzems, K., Serrano, P., Michael, G., Reto, H., Wuthrich, K.

Assembly

YP 557733.1

Entity

1. YP 557733.1 (polymer, Thiol state: all disulfide bound), 145 monomers, 15399.06 Da Detail

IPKHPDSEAV APDPFNPAAT QLLDDTSWVL SAWKQADGTA RAVPSADQGA PITLTLSTST GQRHASGFSG CNRYMGSYAL KDGKLSFGTL GGTRMACMTP GGQIEGAYLN ALTHIDRTGV QMRAPQQMQL VLDNGDTLTF DRSTR

Formula weight

15399.06 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS71:SG	1:CYS97:SG

Source organism

Paraburkholderia xenovorans

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.5 %, Completeness (bb): 84.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.5 % (1421 of 1571)	97.8 % (791 of 809)	78.6 % (480 of 611)	99.3 % (150 of 151)
Backbone	84.5 % (720 of 852)	97.6 % (289 of 296)	70.5 % (296 of 420)	99.3 % (135 of 136)
Sidechain	97.8 % (830 of 849)	97.9 % (502 of 513)	97.5 % (313 of 321)	100.0 % (15 of 15)
Aromatic	94.0 % (94 of 100)	96.0 % (48 of 50)	91.7 % (44 of 48)	100.0 % (2 of 2)
Methyl	97.3 % (146 of 150)	96.0 % (72 of 75)	98.7 % (74 of 75)

1. YP 557733.1

IPKHPDSEAV APDPFNPAAT QLLDDTSWVL SAWKQADGTA RAVPSADQGA PITLTLSTST GQRHASGFSG CNRYMGSYAL KDGKLSFGTL GGTRMACMTP GGQIEGAYLN ALTHIDRTGV QMRAPQQMQL VLDNGDTLTF DRSTR

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LA7, Strand ID: A Detail

Release date

2011-03-24

Related entities 1. YP 557733.1, : 1 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 5D APSY-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 4D APSY-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 5D APSY-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		4.5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17509_2la7.nef
Input source #2: Coordindates	2la7.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:71:CYS:SG	A:97:CYS:SG	oxidized, CA 56.186, CB 38.762 ppm	oxidized, CA 57.161, CB 40.888 ppm	2.317

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
IPKHPDSEAVAPDPFNPAATQLLDDTSWVLSAWKQADGTARAVPSADQGAPITLTLSTSTGQRHASGFSGCNRYMGSYALKDGKLSFGTLGGTRMACMTP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IPKHPDSEAVAPDPFNPAATQLLDDTSWVLSAWKQADGTARAVPSADQGAPITLTLSTSTGQRHASGFSGCNRYMGSYALKDGKLSFGTLGGTRMACMTP

-------110-------120-------130-------140-----
GGQIEGAYLNALTHIDRTGVQMRAPQQMQLVLDNGDTLTFDRSTR
|||||||||||||||||||||||||||||||||||||||||||||
GGQIEGAYLNALTHIDRTGVQMRAPQQMQLVLDNGDTLTFDRSTR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	145	0	0	100.0

Content subtype: combined_17509_2la7.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	1430		100.0 (chain: A, length: 145)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2907 (1)	noe	100.0 (chain: A, length: 145)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 809
  - ¹³C chemical shifts: 462
  - ¹⁵N chemical shifts: 159
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 100.0%
- Total number of restraints: 2907
- Weight of restraints: 1.0 (2907)
- Potential type of restraints: upper-bound-parabolic (2907)
- Range of distance target values: 2.45, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Pilot Secretin MxiM fold, PX10320C