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Found 1 Document (0.604 seconds)

BMRB: 15622

2JOB

Solution structure of an antilipopolysaccharide factor from shrimp

Authors

Yang, Y., Boze, H., Chemardin, P., Padilla, A., Moulin, G., Tassanakajon, A., Pugniere, M., Roquet, F., Gueguen, Y., Bachere, E., Aumelas, A.

Assembly

antilipopolysaccharide factor

Entity

1. antilipopolysaccharide factor (polymer, Thiol state: free and disulfide bound), 102 monomers, 11515.05 Da Detail

EAYVQGWEAV AAAVASKIVG LWRNEKTELL GHECKFTVKP YLKRFQVYYK GRMWCPGWTA IRGEASTRSQ SGVAGKTAKD FVRKAFQKGL ISQQEANQWL SS

Formula weight

11515.05 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS34:SG	1:CYS55:SG

Source organism

Penaeus monodon

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 84.2 %, Completeness (bb): 92.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	84.2 % (631 of 749)	84.6 % (537 of 635)	82.5 % (94 of 114)
Backbone	92.9 % (289 of 311)	96.2 % (203 of 211)	86.0 % (86 of 100)
Sidechain	78.1 % (342 of 438)	78.8 % (334 of 424)	57.1 % (8 of 14)
Aromatic	97.3 % (71 of 73)	97.1 % (66 of 68)	100.0 % (5 of 5)
Methyl	96.1 % (49 of 51)	96.1 % (49 of 51)

1. antilipopolysaccharide factor

EAYVQGWEAV AAAVASKIVG LWRNEKTELL GHECKFTVKP YLKRFQVYYK GRMWCPGWTA IRGEASTRSQ SGVAGKTAKD FVRKAFQKGL ISQQEANQWL SS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
1	ALF	natural abundance		1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.9

#	Name	Isotope labeling	Type	Concentration
2	ALF	[U-99% 15N]		1 mM

Protein Blocks Logo

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

Release date

2008-09-18

Citation

Localization of anti-lipopolysaccharide factor (ALFPm3) in tissues of the black tiger shrimp, Penaeus monodon, and characterization of its binding properties
Somboonwiwat, K., Bachere, E., Rimphanitchayakit, V., Tassanakajon, A.
Dev. Comp. Immunol. (2008), 32, 1170-1176, PubMed 18466970 , DOI 10.1016/j.dci.2008.03.008 , Abstract

Related entities 1. antilipopolysaccharide factor, : 1 : 7 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15622_2job.nef
Input source #2: Coordindates	2job.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:34:CYS:SG	A:55:CYS:SG	unknown	unknown	2.019

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
EAYVQGWEAVAAAVASKIVGLWRNEKTELLGHECKFTVKPYLKRFQVYYKGRMWCPGWTAIRGEASTRSQSGVAGKTAKDFVRKAFQKGLISQQEANQWL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EAYVQGWEAVAAAVASKIVGLWRNEKTELLGHECKFTVKPYLKRFQVYYKGRMWCPGWTAIRGEASTRSQSGVAGKTAKDFVRKAFQKGLISQQEANQWL

--
SS
||
SS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	102	0	0	100.0

Content subtype: combined_15622_2job.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	611		97.1 (chain: A, length: 102)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1150 (1)	noe	95.1 (chain: A, length: 102)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	1138 (1)	noe	95.1 (chain: A, length: 102)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	12 (1)	hbond	13.7 (chain: A, length: 102)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	88 (88)	.	76.5 (chain: A, length: 102)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 521
  - ¹⁵N chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	635	521	82.0
¹⁵N chemical shifts	120	90	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	211	203	96.2
¹⁵N chemical shifts	100	83	83.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	424	318	75.0
¹⁵N chemical shifts	20	7	35.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	49	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	66	97.1
¹⁵N chemical shifts	5	5	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 95.1%
- Total number of restraints: 1150
- Weight of restraints: 1.0 (1150)
- Potential type of restraints: square-well-parabolic (1150)
- Range of distance target values: 1.7, 5.9 (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
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 95.1%
  - Total number of restraints: 1138
  - Weight of restraints: 1.0 (1138)
  - Potential type of restraints: square-well-parabolic (1138)
  - Range of distance target values: 1.7, 5.9 (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
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 13.7%
    - Total number of restraints: 12
    - Weight of restraints: 1.0 (12)
    - Potential type of restraints: square-well-parabolic (12)
    - Range of distance target values: 2.15, 2.15 (Å)
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 76.5%
- Total number of restraints: 88
- Total number of restraints per polymer type: 88
- Weight of restraints: 1.0 (88)
- Potential type of restraints: square-well-parabolic (88)
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ALF, endotoxin, Lipid A binding protein

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Found 1 Document (0.604 seconds)

BMRB: 15622

Sample #1

Sample #2

Related entities 1. antilipopolysaccharide factor, : 1 : 7 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail