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BMRB: 19632

2MHG

NMR structure of protein NP_254181.1 from Pseudomonas aeruginosa PA01

Authors

Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.

Assembly

hypothetical protein BACUNI 03114 from Bacteroides uniformis ATCC 8492

Entity

1. hypothetical protein BACUNI 03114 from Bacteroides uniformis ATCC 8492 (polymer, Thiol state: all free), 75 monomers, 8495.309 Da Detail

GADDDAPSGE PDVTIRQEGD KTIQEYRVNG FLYAIKVVPK HGKPYFLVRA DGSDGNFIRS DQPDKLIPQW EIFSW

Formula weight

8495.309 Da

Source organism

Pseudomonas aeruginosa

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 85.6 %, Completeness (bb): 79.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.6 % (757 of 884)	95.0 % (440 of 463)	70.9 % (244 of 344)	94.8 % (73 of 77)
Backbone	79.9 % (350 of 438)	96.0 % (145 of 151)	64.2 % (140 of 218)	94.2 % (65 of 69)
Sidechain	92.0 % (473 of 514)	94.6 % (295 of 312)	87.6 % (170 of 194)	100.0 % (8 of 8)
Aromatic	66.3 % (61 of 92)	78.3 % (36 of 46)	52.3 % (23 of 44)	100.0 % (2 of 2)
Methyl	98.5 % (67 of 68)	100.0 % (34 of 34)	97.1 % (33 of 34)

1. entity

GADDDAPSGE PDVTIRQEGD KTIQEYRVNG FLYAIKVVPK HGKPYFLVRA DGSDGNFIRS DQPDKLIPQW EIFSW

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-99% 13C; U-98% 15N]		0.6 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium chloride	natural abundance		50 mM
8	sodium azide	natural abundance		5 mM
9	entity	[U-15N; U-2H]		0.6 mM

LACS Plot; CA

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-12-19

Citation

Anti-quorum sensing activity in Pseudomonas aeruginosa PA01 of benzimidazolium salts: electronic, spectral and structural investigations as theoretical approach
Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.
J. Biomol. Struct. Dyn. (2021), 1-12, PubMed 33645444 , DOI 10.1080/07391102.2021.1890222 , Abstract

Related entities 1. hypothetical protein BACUNI 03114 from Bacteroides uniformis ATCC 8492, : 1 entities Detail

Experiments performed 8 experiments Detail

1 APSY 4D-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-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM

2 APSY 5D-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-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM

3 APSY 5D-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-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM

4 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-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM

5 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-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM

6 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-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM

7 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-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM

8 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
5	entity	[U-99% 13C; U-98% 15N]		0.6 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium chloride	natural abundance		50 mM
8	sodium azide	natural abundance		5 mM
9	entity	[U-15N; U-2H]		0.6 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19632_2mhg.nef
Input source #2: Coordindates	2mhg.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-----
GADDDAPSGEPDVTIRQEGDKTIQEYRVNGFLYAIKVVPKHGKPYFLVRADGSDGNFIRSDQPDKLIPQWEIFSW
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GADDDAPSGEPDVTIRQEGDKTIQEYRVNGFLYAIKVVPKHGKPYFLVRADGSDGNFIRSDQPDKLIPQWEIFSW

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

-------110-------120-------130-------140-------150-------160-------170-----
GADDDAPSGEPDVTIRQEGDKTIQEYRVNGFLYAIKVVPKHGKPYFLVRADGSDGNFIRSDQPDKLIPQWEIFSW
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GADDDAPSGEPDVTIRQEGDKTIQEYRVNGFLYAIKVVPKHGKPYFLVRADGSDGNFIRSDQPDKLIPQWEIFSW
--------10--------20--------30--------40--------50--------60--------70-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	75	0	0	100.0
B	B	75	0	0	100.0

Content subtype: combined_19632_2mhg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	762		97.3 (chain: A, length: 75)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3787 (1)	noe	94.7 (chain: A, length: 75), 94.7 (chain: B, length: 75)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 97.3%
- Total number of assignments
  - ¹H chemical shifts: 448
  - ¹³C chemical shifts: 241
  - ¹⁵N chemical shifts: 73
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 94.7%
  - Entity_assembly_ID: B, Chain length: 75, Sequence coverage: 94.7%
- Total number of restraints: 3780
- Weight of restraints: 1.0 (3780)
- Potential type of restraints: upper-bound-parabolic (3780)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords human gut microbiome secreted protein, Protein dimer, Protein of unknown function