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BMRB: 18329

2LQU

Structure of decorbin-binding protein A from Borrelia burgdorferi

Authors

Assembly

DBPA

Entity

1. DBPA (polymer, Thiol state: all disulfide bound), 336 monomers, 37031.83 Da Detail

SAGLTGATKI RLERSAKDIT DEIDAIKKDA ALKGVNFDAF KDKKTGSGVS ENPFILEAKV RATTVAEKFV IAIEEEATKL KETGSSGEFS AMYDLMFEVS KPLQKLGIQE MTKTVSDAAE ENPPTTAQGV LEIAKKMREK LQRVHTKNYC TLKKKENSTF TDEKCKNNSA GLTGATKIRL ERSAKDITDE IDAIKKDAAL KGVNFDAFKD KKTGSGVSEN PFILEAKVRA TTVAEKFVIA IEEEATKLKE TGSSGEFSAM YDLMFEVSKP LQKLGIQEMT KTVSDAAEEN PPTTAQGVLE IAKKMREKLQ RVHTKNYCTL KKKENSTFTD EKCKNN

Formula weight

37031.83 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS150:SG	1:CYS165:SG

Source organism

Borreliella burgdorferi B31

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, RDCs

Chem. Shift Complete

Sequence coverage: 62.2 %, Completeness: 50.2 %, Completeness (bb): 57.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	50.2 % (1956 of 3896)	48.7 % (993 of 2038)	50.5 % (762 of 1508)	57.4 % (201 of 350)
Backbone	57.7 % (1154 of 2000)	58.7 % (400 of 682)	56.1 % (555 of 990)	60.7 % (199 of 328)
Sidechain	44.8 % (991 of 2214)	43.7 % (593 of 1356)	47.4 % (396 of 836)	9.1 % (2 of 22)
Aromatic	20.6 % (37 of 180)	22.2 % (20 of 90)	18.9 % (17 of 90)
Methyl	58.5 % (213 of 364)	60.4 % (110 of 182)	56.6 % (103 of 182)

1. DBPA

SAGLTGATKI RLERSAKDIT DEIDAIKKDA ALKGVNFDAF KDKKTGSGVS ENPFILEAKV RATTVAEKFV IAIEEEATKL KETGSSGEFS AMYDLMFEVS KPLQKLGIQE MTKTVSDAAE ENPPTTAQGV LEIAKKMREK LQRVHTKNYC TLKKKENSTF TDEKCKNNSA GLTGATKIRL ERSAKDITDE IDAIKKDAAL KGVNFDAFKD KKTGSGVSEN PFILEAKVRA TTVAEKFVIA IEEEATKLKE TGSSGEFSAM YDLMFEVSKP LQKLGIQEMT KTVSDAAEEN PPTTAQGVLE IAKKMREKLQ RVHTKNYCTL KKKENSTFTD EKCKNN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample

#	Name	Isotope labeling	Type	Concentration
1	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		50 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details anisotropic sample in 5% neutral gel

#	Name	Isotope labeling	Type	Concentration
5	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
6	sodium phosphate	natural abundance		50 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		90 %
9	polyacrylamide	natural abundance		5 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2LQU, Strand ID: A Detail

RDC

215 RDC values in 2 lists
Field strength (¹H) 800 MHz, Pressure 1 atm, Temperature 298 K, pH 6.5 Detail

Release date

2013-01-14

Citation

Solution structure of decorin-binding protein A from Borrelia burgdorferi
Wang, X.
Biochemistry (2012), 51, 8353-8362, PubMed 22985470 , DOI 10.1021/bi3007093 , Abstract

Related entities 1. DBPA, : 2 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent Inova 800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample

#	Name	Isotope labeling	Type	Concentration
1	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		50 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

2 3D HNCACB

Instrument

Agilent Inova 800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample

#	Name	Isotope labeling	Type	Concentration
1	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		50 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

3 3D CBCA(CO)NH

Instrument

Agilent Inova 800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample

#	Name	Isotope labeling	Type	Concentration
1	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		50 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

4 3D 1H-15N NOESY

Instrument

Agilent Inova 800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample

#	Name	Isotope labeling	Type	Concentration
1	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		50 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

5 3D 1H-13C NOESY aliphatic

Instrument

Agilent Inova 800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample

#	Name	Isotope labeling	Type	Concentration
1	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		50 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

6 3D HCCH-TOCSY

Instrument

Agilent Inova 800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample

#	Name	Isotope labeling	Type	Concentration
1	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		50 mM
3	D2O	natural abundance		10 %
4	H2O	natural abundance		90 %

7 J-modulated 15N HSQC

Instrument

Agilent Inova 800 - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details anisotropic sample in 5% neutral gel

#	Name	Isotope labeling	Type	Concentration
5	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
6	sodium phosphate	natural abundance		50 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		90 %
9	polyacrylamide	natural abundance		5 %

8 JNC-modulated 15N HSQC

Instrument

Agilent Inova 800 - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details anisotropic sample in 5% neutral gel

#	Name	Isotope labeling	Type	Concentration
5	DBPA	[U-100% 13C; U-100% 15N]		0.8 mM
6	sodium phosphate	natural abundance		50 mM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		90 %
9	polyacrylamide	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18329_2lqu.nef
Input source #2: Coordindates	2lqu.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:173:CYS:SG	A:188:CYS:SG	oxidized, CA 58.4, CB 38.6 ppm	unknown	2.021

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

-----30--------40--------50--------60--------70--------80--------90-------100-------110-------120---
SAGLTGATKIRLERSAKDITDEIDAIKKDAALKGVNFDAFKDKKTGSGVSENPFILEAKVRATTVAEKFVIAIEEEATKLKETGSSGEFSAMYDLMFEVS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SAGLTGATKIRLERSAKDITDEIDAIKKDAALKGVNFDAFKDKKTGSGVSENPFILEAKVRATTVAEKFVIAIEEEATKLKETGSSGEFSAMYDLMFEVS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----130-------140-------150-------160-------170-------180-------190-
KPLQKLGIQEMTKTVSDAAEENPPTTAQGVLEIAKKMREKLQRVHTKNYCTLKKKENSTFTDEKCKNN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KPLQKLGIQEMTKTVSDAAEENPPTTAQGVLEIAKKMREKLQRVHTKNYCTLKKKENSTFTDEKCKNN
-------110-------120-------130-------140-------150-------160--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	168	0	0	100.0

Content subtype: combined_18329_2lqu.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	1535		98.2 (chain: A, length: 168)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2045 (1)	noe	95.8 (chain: A, length: 168)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	210 (210)	.	70.2 (chain: A, length: 168)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 98.2%
- Total number of assignments
  - ¹H chemical shifts: 746
  - ¹³C chemical shifts: 633
  - ¹⁵N chemical shifts: 156
- 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: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 95.8%
- Total number of restraints: 2045
- Weight of restraints: 1.0 (2045)
- Potential type of restraints: square-well-parabolic (2045)
- Range of distance target values: 2.67, 4.4 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 70.2%
- Total number of restraints: 210
- Total number of restraints per polymer type: 210
- Weight of restraints: 1.0 (210)
- Potential type of restraints: square-well-parabolic (210)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords GAG-binding protein, helical bundle protein, Lyme disease