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BMRB: 18571

2LVI

Solution structure of apo-Phl p 7

Authors

Henzl, M.T., Tanner, J.J.

Assembly

apo-Phl p 7

Entity

1. apo-Phl p 7 (polymer), 77 monomers, 8545.428 Da Detail

ADDMERIFKR FDTNGDGKIS LSELTDALRT LGSTSADEVQ RMMAEIDTDG DGFIDFNEFI SFCNANPGLM KDVAKVF

Formula weight

8545.428 Da

Source organism

Phleum pratense

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.7 %, Completeness: 92.2 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.2 % (796 of 863)	94.6 % (421 of 445)	87.8 % (296 of 337)	97.5 % (79 of 81)
Backbone	97.6 % (449 of 460)	96.2 % (153 of 159)	98.7 % (222 of 225)	97.4 % (74 of 76)
Sidechain	88.0 % (417 of 474)	93.7 % (268 of 286)	78.7 % (144 of 183)	100.0 % (5 of 5)
Aromatic	40.0 % (28 of 70)	80.0 % (28 of 35)	0.0 % (0 of 35)
Methyl	97.3 % (72 of 74)	97.3 % (36 of 37)	97.3 % (36 of 37)

1. Phl p 7

ADDMERIFKR FDTNGDGKIS LSELTDALRT LGSTSADEVQ RMMAEIDTDG DGFIDFNEFI SFCNANPGLM KDVAKVF

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

LACS Plot; CA

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.5 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-09-30

Citation

Solution structures of polcalcin Phl p 7 in three ligation states: Apo-, hemi-Mg2+-bound, and fully Ca2+-bound
Henzl, M.T., Sirianni, A.G., Wycoff, W.G., Tan, A., Tanner, J.J.
Proteins (2013), 81, 300-315, PubMed 23011803 , DOI 10.1002/prot.24186 , Abstract

Related entities 1. apo-Phl p 7, : 1 : 5 : 1 : 207 entities Detail

Experiments performed 17 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

4 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

5 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

6 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

7 3D HCACOCANH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

8 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

9 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

10 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

11 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

12 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

13 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

14 2D HBCBCGCDHD

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

15 2D HBCBCGCDCEHE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

16 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

17 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.5) K, pH 6.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Phl p 7	[U-98% 13C; U-98% 15N]		3 (±0.3) mM
2	sodium chloride	natural abundance		150 (±1.5) mM
3	MES	natural abundance		10 (±0.1) mM
4	D2O	[U-99% 2H]		10 (±1.0) %
5	H2O	natural abundance		90 (±1.0) %
6	sodium azide	natural abundance		0.1 (±0.01) %
7	EDTA	natural abundance		5 (±0.1) mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18571_2lvi.nef
Input source #2: Coordindates	2lvi.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-------
ADDMERIFKRFDTNGDGKISLSELTDALRTLGSTSADEVQRMMAEIDTDGDGFIDFNEFISFCNANPGLMKDVAKVF
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ADDMERIFKRFDTNGDGKISLSELTDALRTLGSTSADEVQRMMAEIDTDGDGFIDFNEFISFCNANPGLMKDVAKVF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	77	0	0	100.0

Content subtype: combined_18571_2lvi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	799		98.7 (chain: A, length: 77)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1756 (1)	noe	98.7 (chain: A, length: 77)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 424
  - ¹³C chemical shifts: 296
  - ¹⁵N chemical shifts: 79
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 77, Sequence coverage: 98.7%
- Total number of restraints: 1755
- Weight of restraints: 1.0 (1755)
- Potential type of restraints: upper-bound-parabolic (1755)
- Range of distance target values: 2.32, 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

Keywords calcium-binding protein, EF-hand protein, polcalcin, protein