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BMRB: 15134

2JNZ

Solution structure of phl p 3, a major allergen from timothy grass pollen

Authors

Schweimer, K., Matecko, I., Roesch, P.

Assembly

phl p 3

Entity

1. phl p 3 (polymer, Thiol state: not present), 108 monomers, 12225.68 Da Detail

RGSHHHHHHG SAVQVTFTVQ KGSDPKKLVL DIKYTRPGDS LAEVELRQHG SEEWEPLTKK GNVWEVKSSK PLVGPFNFRF MSKGGMRNVF DEVIPTAFSI GKTYKPEE

Formula weight

12225.68 Da

Source organism

Phleum pratense

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.6 %, Completeness: 85.0 %, Completeness (bb): 90.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.0 % (1092 of 1285)	89.0 % (600 of 674)	78.9 % (396 of 502)	88.1 % (96 of 109)
Backbone	90.4 % (573 of 634)	90.9 % (199 of 219)	90.4 % (284 of 314)	89.1 % (90 of 101)
Sidechain	81.6 % (611 of 749)	88.1 % (401 of 455)	71.3 % (204 of 286)	75.0 % (6 of 8)
Aromatic	41.4 % (53 of 128)	75.0 % (48 of 64)	4.8 % (3 of 62)	100.0 % (2 of 2)
Methyl	93.6 % (88 of 94)	100.0 % (47 of 47)	87.2 % (41 of 47)

1. phl p 3

RGSHHHHHHG SAVQVTFTVQ KGSDPKKLVL DIKYTRPGDS LAEVELRQHG SEEWEPLTKK GNVWEVKSSK PLVGPFNFRF MSKGGMRNVF DEVIPTAFSI GKTYKPEE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details Pf1 phage solution for RDC measurements

#	Name	Isotope labeling	Type	Concentration
5	phl p 3	[U-95% 13C; U-95% 15N]		1 mM
6	Pf1 phage	natural abundance		10 mg/mL
7	DTT	natural abundance		1 mM
8	NaCl	natural abundance		100 mM
9	phosphate buffer	natural abundance		20 mM

LACS Plot; CA

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.85 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2008-07-27

Citation

Solution structure of Phl p 3, a major allergen from timothy grass pollen
Schweimer, K., Petersen, A., Suck, R., Becker, W., Roesch, P., Matecko, I.
Biol. Chem. (2008), 389, 919-923, PubMed 18627309 , DOI 10.1515/BC.2008.102 , Abstract

Related entities 1. phl p 3, : 1 : 2 : 133 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 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

3 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

4 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 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

5 3D HNCO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

6 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

7 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 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

11 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	phl p 3	[U-95% 13C; U-95% 15N]		2 mM
2	DTT	natural abundance		1 mM
3	NaCl	natural abundance		100 mM
4	phosphate buffer	natural abundance		20 mM

12 2D 1H-15N IPAP

Instrument

Bruker DRX - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details Pf1 phage solution for RDC measurements

#	Name	Isotope labeling	Type	Concentration
5	phl p 3	[U-95% 13C; U-95% 15N]		1 mM
6	Pf1 phage	natural abundance		10 mg/mL
7	DTT	natural abundance		1 mM
8	NaCl	natural abundance		100 mM
9	phosphate buffer	natural abundance		20 mM

13 3D HA(CO)NH-J

Instrument

Bruker DRX - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details Pf1 phage solution for RDC measurements

#	Name	Isotope labeling	Type	Concentration
5	phl p 3	[U-95% 13C; U-95% 15N]		1 mM
6	Pf1 phage	natural abundance		10 mg/mL
7	DTT	natural abundance		1 mM
8	NaCl	natural abundance		100 mM
9	phosphate buffer	natural abundance		20 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15134_2jnz.nef
Input source #2: Coordindates	2jnz.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--------80--------90-------100
RGSHHHHHHGSAVQVTFTVQKGSDPKKLVLDIKYTRPGDSLAEVELRQHGSEEWEPLTKKGNVWEVKSSKPLVGPFNFRFMSKGGMRNVFDEVIPTAFSI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RGSHHHHHHGSAVQVTFTVQKGSDPKKLVLDIKYTRPGDSLAEVELRQHGSEEWEPLTKKGNVWEVKSSKPLVGPFNFRFMSKGGMRNVFDEVIPTAFSI

--------
GKTYKPEE
||||||||
GKTYKPEE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	108	0	0	100.0

Content subtype: combined_15134_2jnz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1069		90.7 (chain: A, length: 108)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3036 (1)	noe	90.7 (chain: A, length: 108)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	66 (1)	hbond	34.3 (chain: A, length: 108)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	25 (25)	.	22.2 (chain: A, length: 108)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	138 (138)	.	77.8 (chain: A, length: 108)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 90.7%
- Total number of assignments
  - ¹H chemical shifts: 588
  - ¹³C chemical shifts: 386
  - ¹⁵N chemical shifts: 95
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 90.7%
- Total number of restraints: 3031
- Weight of restraints: 1.0 (3031)
- Potential type of restraints: square-well-parabolic (3031)
- Range of distance target values: 1.25, 3.0 (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_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 34.3%
  - Total number of restraints: 66
  - Weight of restraints: 1.0 (66)
  - Potential type of restraints: square-well-parabolic (66)
  - Range of distance target values: 1.15, 1.55 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 22.2%
- Total number of restraints: 25
- Total number of restraints per polymer type: 25
- Weight of restraints: 1.0 (25)
- Potential type of restraints: square-well-parabolic (25)
- Dihedral angle restraints per residue

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 77.8%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
RGSHHHHHHGSAVQVTFTVQKGSDPKKLVLDIKYTRPGDSLAEVELRQHGSEEWEPLTKKGNVWEVKSSKPLVGPFNFRFMSKGGMRNVFDEVIPTAFSI
            ||||||||| ||||||||||||||  |||||||||||||| ||||||| |||||||   |||||||||||||||||||||||||||||
............VQVTFTVQK.SDPKKLVLDIKYTR..DSLAEVELRQHGSE.WEPLTKK.NVWEVKS...LVGPFNFRFMSKGGMRNVFDEVIPTAFSI
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--------
GKTYKPEE
||||    
GKTY    
----

Total number of restraints: 138
Potential type of restraints: undefined (138)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords allergen, timothy grass pollen