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Found 1 Document (0.755 seconds)

BMRB: 25859

2N8R

Productive complex between MMP-12 and synthetic triple-helical collagen, revealed through paramagnetic NMR

Authors

Prior, S.H., VanDoren, S.R.

Assembly

complex between MMP-12 and synthetic triple-helical collagen

Entity

1. MMP-12 (polymer, Thiol state: not present), 164 monomers, 18211.19 Da Detail

FREMPGGPVW RKHYITYRIN NYTPDMNRED VDYAIRKAFQ VWSNVTPLKF SKINTGMADI LVVFARGAHG DFHAFDGKGG ILAHAFGPGS GIGGDAHFDE DEFWTTHSGG TNLFLTAVHE IGHSLGLGHS SDPKAVMFPT YKYVDINTFR LSADDIRGIQ SLYG

2. THP (polymer, Thiol state: not present), 36 monomers, 3291.447 × 3 Da Detail

GPXGPXGPXG PXGPPGVVGE QGEQGPXGPX GPXGPX

3. complex between MMP-12 and synthetic triple-helical collagen, entity ZN (non-polymer), 65.409 × 2 Da
4. complex between MMP-12 and synthetic triple-helical collagen, entity CA (non-polymer), 40.078 × 3 Da
5. complex between MMP-12 and synthetic triple-helical collagen, entity HOH (water), 18.015 Da

Total weight

28336.584 Da

Max. entity weight

18211.19 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

Rigid-body docking, Conformer selection

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.0 %, Completeness: 76.3 %, Completeness (bb): 81.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.3 % (1636 of 2144)	74.7 % (828 of 1108)	75.8 % (642 of 847)	87.8 % (166 of 189)
Backbone	81.8 % (914 of 1118)	83.2 % (332 of 399)	78.7 % (428 of 544)	88.0 % (154 of 175)
Sidechain	72.5 % (860 of 1186)	70.0 % (496 of 709)	76.0 % (352 of 463)	85.7 % (12 of 14)
Aromatic	64.9 % (161 of 248)	66.1 % (82 of 124)	62.8 % (76 of 121)	100.0 % (3 of 3)
Methyl	85.7 % (144 of 168)	89.3 % (75 of 84)	82.1 % (69 of 84)

1. MMP-12

FREMPGGPVW RKHYITYRIN NYTPDMNRED VDYAIRKAFQ VWSNVTPLKF SKINTGMADI LVVFARGAHG DFHAFDGKGG ILAHAFGPGS GIGGDAHFDE DEFWTTHSGG TNLFLTAVHE IGHSLGLGHS SDPKAVMFPT YKYVDINTFR LSADDIRGIQ SLYG

2. THP

GPXGPXGPXG PXGPPGVVGE QGEQGPXGPX GPXGPX

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 299 (±1) K, pH 6.6 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	MMP-12	[U-99% 15N]	protein	0.4 mM
2	THP	TOAC labelled in P5 position		0.6 mM

Sample #2

Solvent system 90% H2O/10% D2O, Temperature 299 (±1) K, pH 6.6 (±0.05)

#	Name	Isotope labeling	Type	Concentration
3	MMP-12	[U-100% 12C; U-100% 15N; U-100% 2H; U-100% 13CH3]	protein	0.25 mM
4	THP	TOAC labelled in P8' position		0.38 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.32 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.32 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 1 models in PDB: 2N8R, Strand ID: A, B, C, D Detail

Release date

2016-02-21

Citation

1H, 13C, and 15N peak assignments and secondary structure of human macrophage metalloelastase (MMP-12) in its inhibitor-free state
Bhaskaran, R., VanDoren, S.R.
J. Biomol. NMR (2006), 36 Suppl 1, 55-55, PubMed 16855860 , DOI 10.1007/s10858-006-9035-8 , Abstract

Related entities 1. MMP-12, : 1 : 90 entities Detail

Related entities 2. THP, : 58 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_25859_2n8r.nef
Input source #2: Coordindates	2n8r.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Distance (Å)
A:71:ASP:OD1	F:null:ZN:ZN	1.79
E:null:ZN:ZN	J:null:HOH:O	1.875
D:16:GLY:O	E:null:ZN:ZN	1.89
D:15:PRO:O	E:null:ZN:ZN	2.057
A:69:HIS:NE2	F:null:ZN:ZN	2.099
A:84:HIS:NE2	F:null:ZN:ZN	2.1
A:97:HIS:ND1	F:null:ZN:ZN	2.1
A:119:HIS:NE2	E:null:ZN:ZN	2.1
A:123:HIS:NE2	E:null:ZN:ZN	2.1
A:129:HIS:NE2	E:null:ZN:ZN	2.1
A:71:ASP:OD2	F:null:ZN:ZN	2.101
A:25:ASP:OD2	I:null:CA:CA	2.299
A:102:GLU:OE2	G:null:CA:CA	2.299
A:25:ASP:OD1	I:null:CA:CA	2.299
A:95:ASP:OD1	H:null:CA:CA	2.3
A:59:ASP:O	H:null:CA:CA	2.3
A:100:GLU:OE2	I:null:CA:CA	2.3
A:79:GLY:O	G:null:CA:CA	2.3
A:91:GLY:O	H:null:CA:CA	2.3
A:81:ILE:O	G:null:CA:CA	2.3
A:76:ASP:OD1	G:null:CA:CA	2.3
A:77:GLY:O	G:null:CA:CA	2.3
A:99:ASP:OD2	G:null:CA:CA	2.3
A:102:GLU:O	I:null:CA:CA	2.3
A:93:GLY:O	H:null:CA:CA	2.301
A:100:GLU:O	I:null:CA:CA	2.301

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	3	HYP	4-HYDROXYPROLINE	Coordinates
B	6	HYP	4-HYDROXYPROLINE	Coordinates
B	9	HYP	4-HYDROXYPROLINE	Coordinates
B	12	HYP	4-HYDROXYPROLINE	Coordinates
B	27	HYP	4-HYDROXYPROLINE	Coordinates
B	30	HYP	4-HYDROXYPROLINE	Coordinates
B	33	HYP	4-HYDROXYPROLINE	Coordinates
B	36	HYP	4-HYDROXYPROLINE	Coordinates
C	39	HYP	4-HYDROXYPROLINE	Coordinates
C	42	HYP	4-HYDROXYPROLINE	Coordinates
C	45	HYP	4-HYDROXYPROLINE	Coordinates
C	48	HYP	4-HYDROXYPROLINE	Coordinates
C	63	HYP	4-HYDROXYPROLINE	Coordinates
C	66	HYP	4-HYDROXYPROLINE	Coordinates
C	69	HYP	4-HYDROXYPROLINE	Coordinates
C	72	HYP	4-HYDROXYPROLINE	Coordinates
D	75	HYP	4-HYDROXYPROLINE	Coordinates
D	78	HYP	4-HYDROXYPROLINE	Coordinates
D	81	HYP	4-HYDROXYPROLINE	Coordinates
D	84	HYP	4-HYDROXYPROLINE	Coordinates
D	99	HYP	4-HYDROXYPROLINE	Coordinates
D	102	HYP	4-HYDROXYPROLINE	Coordinates
D	105	HYP	4-HYDROXYPROLINE	Coordinates
D	108	HYP	4-HYDROXYPROLINE	Coordinates
E	1	CA	CALCIUM ION	None
E	2	CA	CALCIUM ION	None
E	3	CA	CALCIUM ION	None
F	1	ZN	ZINC ION	None
F	2	ZN	ZINC ION	None

Sequence alignments

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

100-----110-------120-------130-------140-------150-------160-------170-------180-------190-------20
FREMPGGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FREMPGGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------210-------220-------230-------240-------250-------260---
DEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
-------110-------120-------130-------140-------150-------160----

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

--------10--------20--------30------
GPXGPXGPXGPXGPPGVVGEQGEQGPXGPXGPXGPX
||||||||||||||||||||||||||||||||||||
GPXGPXGPXGPXGPPGVVGEQGEQGPXGPXGPXGPX

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

--40--------50--------60--------70--
GPXGPXGPXGPXGPPGVVGEQGEQGPXGPXGPXGPX
||||||||||||||||||||||||||||||||||||
GPXGPXGPXGPXGPPGVVGEQGEQGPXGPXGPXGPX
--------10--------20--------30------

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

------80--------90-------100--------
GPXGPXGPXGPXGPPGVVGEQGEQGPXGPXGPXGPX
||||||||||||||||||||||||||||||||||||
GPXGPXGPXGPXGPPGVVGEQGEQGPXGPXGPXGPX
--------10--------20--------30------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	164	100.0
B	B	36	100.0
C	C	36	100.0
D	D	36	100.0

Content subtype: combined_25859_2n8r.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	Warning	1599		98.2 (chain: A, length: 164)

Assigned chemical shifts

Saveframe: chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 164, Sequence coverage: 98.2%
- Total number of assignments
  - ¹H chemical shifts: 799
  - ¹³C chemical shifts: 635
  - ¹⁵N chemical shifts: 165
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	964	799	82.9
¹³C chemical shifts	747	635	85.0
¹⁵N chemical shifts	177	165	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	341	330	96.8
¹³C chemical shifts	328	287	87.5
¹⁵N chemical shifts	157	153	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	623	469	75.3
¹³C chemical shifts	419	348	83.1
¹⁵N chemical shifts	20	12	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	77	91.7
¹³C chemical shifts	84	71	84.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	79	63.7
¹³C chemical shifts	121	76	62.8
¹⁵N chemical shifts	3	3	100.0

Keywords MMP-12, Collagenolysis, MMP, matrix petalloproteinase, triple-helical collagen, Chemical Shift Assignment, NMR

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Found 1 Document (0.755 seconds)

BMRB: 25859

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MMP-12, : 1 : 90 entities Detail

Related entities 2. THP, : 58 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 2 contents Detail