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BMRB: 18692

2LXR

Solution structure of HP1264 from Helicobacter pylori

Authors

Assembly

HP1264

Entity

1. HP1264 (polymer, Thiol state: not present), 76 monomers, 8926.258 Da Detail

MKRFDLRPLK AGIFERLEEL IEKEMQPNEV AIFMFEVGDF SNIPKSAEFI QSKGHELLNS LRFNQADWTI VVRKKA

Formula weight

8926.258 Da

Source organism

Helicobacter pylori

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.1 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.1 % (814 of 956)	87.5 % (442 of 505)	81.4 % (301 of 370)	87.7 % (71 of 81)
Backbone	96.2 % (433 of 450)	98.7 % (150 of 152)	94.2 % (212 of 225)	97.3 % (71 of 73)
Sidechain	78.2 % (453 of 579)	82.7 % (292 of 353)	73.9 % (161 of 218)	0.0 % (0 of 8)
Aromatic	24.4 % (21 of 86)	48.8 % (21 of 43)	0.0 % (0 of 42)	0.0 % (0 of 1)
Methyl	85.0 % (68 of 80)	90.0 % (36 of 40)	80.0 % (32 of 40)

1. entity

MKRFDLRPLK AGIFERLEEL IEKEMQPNEV AIFMFEVGDF SNIPKSAEFI QSKGHELLNS LRFNQADWTI VVRKKA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

LACS Plot; CA

Referencing offset: -0.17 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.17 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.07 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: -1.87 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-09-30

Citation

Structural characterization of HP1264 reveals a novel fold for the flavin mononucleotide binding protein
Lee, K., Kim, J., Lee, K., Lee, J., Lee, I., Bae, Y., Lee, B.
Biochemistry (2013), 52, 1583-1593, PubMed 23406339 , DOI 10.1021/bi301714a , Abstract

Related entities 1. HP1264, : 1 : 3 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

2 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

3 3D C(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

4 3D HNCO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

5 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

6 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

7 3D HBHA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

8 3D HN(CO)CA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

9 3D H(CCO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

10 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

11 3D 1H-13C NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

12 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

13 3D HN(CA)CO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	HP1264	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		150 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18692_2lxr.nef
Input source #2: Coordindates	2lxr.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------
MKRFDLRPLKAGIFERLEELIEKEMQPNEVAIFMFEVGDFSNIPKSAEFIQSKGHELLNSLRFNQADWTIVVRKKA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKRFDLRPLKAGIFERLEELIEKEMQPNEVAIFMFEVGDFSNIPKSAEFIQSKGHELLNSLRFNQADWTIVVRKKA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	76	0	0	100.0

Content subtype: combined_18692_2lxr.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	809		100.0 (chain: A, length: 76)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	975 (1)	noe	100.0 (chain: A, length: 76)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	86 (86)	.	73.7 (chain: A, length: 76)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 437
  - ¹³C chemical shifts: 301
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
- Total number of restraints: 975
- Weight of restraints: 1.0 (975)
- Potential type of restraints: upper-bound-parabolic (975)
- Range of distance target values: 2.0, 5.5 (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: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 73.7%
- Total number of restraints: 86
- Total number of restraints per polymer type: 86
- Weight of restraints: 1.0 (86)
- Potential type of restraints: square-well-parabolic (86)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords HP1264