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BMRB: 18083

2LLP

Solution structure of a THP type 1 alpha 1 collagen fragment (772-786)

Authors

Bertini, I., Fragai, M., Luchinat, C., Melikian, M., Toccafondi, M., Lauer, J.L., Fields, G.B.

Assembly

THP type 1 alpha 1 collagen fragment (772-786)

Entity

1. THP type 1 alpha 1 collagen fragment (772-786) (polymer), 18 monomers, 1656.882 × 3 Da Detail

PPGPQGIAGQ RGVVGLPG

Total weight

4970.646 Da

Max. entity weight

1656.882 Da

Source organism

Exptl. method

Refine. method

simulated annealing, minimisation

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 77.8 %, Completeness: 76.6 %, Completeness (bb): 82.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.6 % (141 of 184)	74.5 % (73 of 98)	75.7 % (53 of 70)	93.8 % (15 of 16)
Backbone	82.0 % (82 of 100)	84.2 % (32 of 38)	77.1 % (37 of 48)	92.9 % (13 of 14)
Sidechain	70.8 % (68 of 96)	68.3 % (41 of 60)	73.5 % (25 of 34)	100.0 % (2 of 2)
Methyl	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)

1. entity 1

PPGPQGIAGQ RGVVGLPG

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details NaCl 0.15M, CaCl2 10mM, ZnCl2 0.1 mM, 20 mM tris buffer

#	Name	Isotope labeling	Type	Concentration
1	THP type I collagen	[U-98% 13C; U-98% 15N]		0.4 ~ 0.8 mM
2	sodium chloride	natural abundance		150 mM
3	calcium chloride	natural abundance		10 mM
4	zinc chloride	natural abundance		0.1 mM
5	tris buffer	[U-2H]		20 mM

Protein Blocks Logo

Calculated from 30 models in PDB: 2LLP, Strand ID: A, B, C Detail

Release date

2012-08-28

Citation

Structural basis for matrix metalloproteinase 1-catalyzed collagenolysis
Bertini, I., Fragai, M., Luchinat, C., Melikian, M., Toccafondi, M., Lauer, J.L., Fields, G.B.
J. Am. Chem. Soc. (2012), 134, 2100-2110, PubMed 22239621 , DOI 10.1021/ja208338j , Abstract

Related entities 1. THP type 1 alpha 1 collagen fragment (772-786), : 1 : 6 : 13 : 25 entities Detail

Interaction partners 1. THP type 1 alpha 1 collagen fragment (772-786), : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 5 experiments Detail

1 3D_15N-separated_NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details NaCl 0.15M, CaCl2 10mM, ZnCl2 0.1 mM, 20 mM tris buffer

#	Name	Isotope labeling	Type	Concentration
1	THP type I collagen	[U-98% 13C; U-98% 15N]		0.4 ~ 0.8 mM
2	sodium chloride	natural abundance		150 mM
3	calcium chloride	natural abundance		10 mM
4	zinc chloride	natural abundance		0.1 mM
5	tris buffer	[U-2H]		20 mM

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details NaCl 0.15M, CaCl2 10mM, ZnCl2 0.1 mM, 20 mM tris buffer

#	Name	Isotope labeling	Type	Concentration
1	THP type I collagen	[U-98% 13C; U-98% 15N]		0.4 ~ 0.8 mM
2	sodium chloride	natural abundance		150 mM
3	calcium chloride	natural abundance		10 mM
4	zinc chloride	natural abundance		0.1 mM
5	tris buffer	[U-2H]		20 mM

3 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details NaCl 0.15M, CaCl2 10mM, ZnCl2 0.1 mM, 20 mM tris buffer

#	Name	Isotope labeling	Type	Concentration
1	THP type I collagen	[U-98% 13C; U-98% 15N]		0.4 ~ 0.8 mM
2	sodium chloride	natural abundance		150 mM
3	calcium chloride	natural abundance		10 mM
4	zinc chloride	natural abundance		0.1 mM
5	tris buffer	[U-2H]		20 mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details NaCl 0.15M, CaCl2 10mM, ZnCl2 0.1 mM, 20 mM tris buffer

#	Name	Isotope labeling	Type	Concentration
1	THP type I collagen	[U-98% 13C; U-98% 15N]		0.4 ~ 0.8 mM
2	sodium chloride	natural abundance		150 mM
3	calcium chloride	natural abundance		10 mM
4	zinc chloride	natural abundance		0.1 mM
5	tris buffer	[U-2H]		20 mM

5 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2, Details NaCl 0.15M, CaCl2 10mM, ZnCl2 0.1 mM, 20 mM tris buffer

#	Name	Isotope labeling	Type	Concentration
1	THP type I collagen	[U-98% 13C; U-98% 15N]		0.4 ~ 0.8 mM
2	sodium chloride	natural abundance		150 mM
3	calcium chloride	natural abundance		10 mM
4	zinc chloride	natural abundance		0.1 mM
5	tris buffer	[U-2H]		20 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18083_2llp.nef
Input source #2: Coordindates	2llp.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

--------20--------
PPGPQGIAGQRGVVGLPG
||||||||||||||||||
PPGPQGIAGQRGVVGLPG
--------10--------

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

--------20--------
PPGPQGIAGQRGVVGLPG
||||||||||||||||||
PPGPQGIAGQRGVVGLPG
--------10--------

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

--------20--------
PPGPQGIAGQRGVVGLPG
||||||||||||||||||
PPGPQGIAGQRGVVGLPG
--------10--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	18	0	0	100.0
B	B	18	0	0	100.0
C	C	18	0	0	100.0

Content subtype: combined_18083_2llp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	143		77.8 (chain: C, length: 18)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	458 (1)	noe	88.9 (chain: A, length: 18), 88.9 (chain: B, length: 18), 88.9 (chain: C, length: 18)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	47 (47)	.	94.4 (chain: A, length: 18), 88.9 (chain: B, length: 18), 83.3 (chain: C, length: 18)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 18, Sequence coverage: 77.8%
- Total number of assignments
  - ¹H chemical shifts: 73
  - ¹³C chemical shifts: 55
  - ¹⁵N chemical shifts: 15
- Completeness of assignments
  - Entity_assemble_ID: C
- 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: C

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 88.9%
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 88.9%
  - Entity_assembly_ID: C, Chain length: 18, Sequence coverage: 88.9%
- Total number of restraints: 454
- Weight of restraints: 1.0 (454)
- Potential type of restraints: upper-bound-parabolic (454)
- 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
  - Chain_ID: C
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 94.4%
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 88.9%
  - Entity_assembly_ID: C, Chain length: 18, Sequence coverage: 83.3%
- Total number of restraints: 47
- Total number of restraints per polymer type: 47
- Weight of restraints: 1.0 (47)
- Potential type of restraints: square-well-parabolic (47)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C

Keywords NMR, triple helical peptide