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BMRB: 15361

2JSD

Solution Structure of MMP20 complexed with NNGH

Authors

Arendt, Y., Banci, L., Bertini, I., Cantini, F., Cozzi, R., Del Conte, R., Gonnelli, L.

Assembly

mmp-20

Entity

1. MMP-20 (polymer, Thiol state: not present), 160 monomers, 17476.30 Da Detail

GEPKWKKNTL TYRISKYTPS MSSVEVDKAV EMALQAWSSA VPLSFVRINS GEADIMISFE NGDHGDSYPF DGPRGTLAHA FAPGEGLGGD THFDNAEKWT MGTNGFNLFT VAAHEFGHAL GLAHSTDPSA LMYPTYKYKN PYGFHLPKDD VKGIQALYGP

2. ZN (non-polymer), 65.409 × 2 Da
3. CA (non-polymer), 40.078 × 2 Da
4. NGH (non-polymer), 316.373 Da

Total weight

18003.648 Da

Max. entity weight

17476.3 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.4 %, Completeness: 91.5 %, Completeness (bb): 95.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.5 % (1659 of 1813)	96.9 % (904 of 933)	83.7 % (602 of 719)	95.0 % (153 of 161)
Backbone	95.9 % (900 of 938)	97.2 % (317 of 326)	94.4 % (437 of 463)	98.0 % (146 of 149)
Sidechain	88.5 % (901 of 1018)	96.7 % (587 of 607)	76.9 % (307 of 399)	58.3 % (7 of 12)
Aromatic	54.1 % (118 of 218)	93.6 % (102 of 109)	15.1 % (16 of 106)	0.0 % (0 of 3)
Methyl	99.3 % (141 of 142)	100.0 % (71 of 71)	98.6 % (70 of 71)

1. MMP-20

GEPKWKKNTL TYRISKYTPS MSSVEVDKAV EMALQAWSSA VPLSFVRINS GEADIMISFE NGDHGDSYPF DGPRGTLAHA FAPGEGLGGD THFDNAEKWT MGTNGFNLFT VAAHEFGHAL GLAHSTDPSA LMYPTYKYKN PYGFHLPKDD VKGIQALYGP

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	MMP-20	[U-99% 15N]		0.6 mM
2	Tris			20 mM
3	ZnCl2			0.1 mM
4	CaCl2			5 mM
5	NaCl			300 mM
6	acetohydroxamic acid			0.3 M

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
7	MMP-20	natural abundance		1 mM
8	Tris			20 mM
9	ZnCl2			0.1 mM
10	CaCl2			5 mM
11	NaCl			300 mM
12	acetohydroxamic acid			0.3 M

Sample #3

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

#	Name	Isotope labeling	Type	Concentration
13	MMP-20	[U-13C; U-15N]		0.6 mM
14	Tris			20 mM
15	ZnCl2			0.1 mM
16	CaCl2			5 mM
17	NaCl			300 mM
18	acetohydroxamic acid			0.3 M

Protein Blocks Logo

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

Release date

2008-03-12

Citation

Catalytic domain of MMP20 (Enamelysin) - the NMR structure of a new matrix metalloproteinase
Arendt, Y., Banci, L., Bertini, I., Cantini, F., Cozzi, R., Del Conte, R., Gonnelli, L.
FEBS Lett. (2007), 581, 4723-4726, PubMed 17869250 , DOI 10.1016/j.febslet.2007.08.069 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: O60882 released on 2000-12-01
Title MMP20_HUMAN Entity Matrix metalloproteinase-20

Related entities 1. MMP-20, : 1 : 2 : 279 entities Detail

Experiments performed 9 experiments Detail

1 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	MMP-20	[U-99% 15N]		0.6 mM
2	Tris			20 mM
3	ZnCl2			0.1 mM
4	CaCl2			5 mM
5	NaCl			300 mM
6	acetohydroxamic acid			0.3 M

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	MMP-20	[U-99% 15N]		0.6 mM
2	Tris			20 mM
3	ZnCl2			0.1 mM
4	CaCl2			5 mM
5	NaCl			300 mM
6	acetohydroxamic acid			0.3 M

3 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	MMP-20	[U-99% 15N]		0.6 mM
2	Tris			20 mM
3	ZnCl2			0.1 mM
4	CaCl2			5 mM
5	NaCl			300 mM
6	acetohydroxamic acid			0.3 M

4 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	MMP-20	[U-99% 15N]		0.6 mM
2	Tris			20 mM
3	ZnCl2			0.1 mM
4	CaCl2			5 mM
5	NaCl			300 mM
6	acetohydroxamic acid			0.3 M

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	MMP-20	[U-99% 15N]		0.6 mM
2	Tris			20 mM
3	ZnCl2			0.1 mM
4	CaCl2			5 mM
5	NaCl			300 mM
6	acetohydroxamic acid			0.3 M

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	MMP-20	[U-99% 15N]		0.6 mM
2	Tris			20 mM
3	ZnCl2			0.1 mM
4	CaCl2			5 mM
5	NaCl			300 mM
6	acetohydroxamic acid			0.3 M

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	MMP-20	[U-99% 15N]		0.6 mM
2	Tris			20 mM
3	ZnCl2			0.1 mM
4	CaCl2			5 mM
5	NaCl			300 mM
6	acetohydroxamic acid			0.3 M

8 r2,r1, 15n-noe

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
7	MMP-20	natural abundance		1 mM
8	Tris			20 mM
9	ZnCl2			0.1 mM
10	CaCl2			5 mM
11	NaCl			300 mM
12	acetohydroxamic acid			0.3 M

9 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
13	MMP-20	[U-13C; U-15N]		0.6 mM
14	Tris			20 mM
15	ZnCl2			0.1 mM
16	CaCl2			5 mM
17	NaCl			300 mM
18	acetohydroxamic acid			0.3 M

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15361_2jsd.nef
Input source #2: Coordindates	2jsd.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	None
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)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	Distance restraints
B	2	ZN	ZINC ION	None
C	1	CA	CALCIUM ION	None
C	2	CA	CALCIUM ION	None
D	1	NGH	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID	None

Sequence alignments

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

-----120-------130-------140-------150-------160-------170-------180-------190-------200-------210--
GEPKWKKNTLTYRISKYTPSMSSVEVDKAVEMALQAWSSAVPLSFVRINSGEADIMISFENGDHGDSYPFDGPRGTLAHAFAPGEGLGGDTHFDNAEKWT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GEPKWKKNTLTYRISKYTPSMSSVEVDKAVEMALQAWSSAVPLSFVRINSGEADIMISFENGDHGDSYPFDGPRGTLAHAFAPGEGLGGDTHFDNAEKWT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----220-------230-------240-------250-------260-------270--
MGTNGFNLFTVAAHEFGHALGLAHSTDPSALMYPTYKYKNPYGFHLPKDDVKGIQALYGP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGTNGFNLFTVAAHEFGHALGLAHSTDPSALMYPTYKYKNPYGFHLPKDDVKGIQALYGP
-------110-------120-------130-------140-------150-------160

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	160	0	0	100.0

Content subtype: combined_15361_2jsd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1650		99.4 (chain: A, length: 160)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2780 (1)	noe	98.8 (chain: A, length: 160)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Error	7 (1)	undefined	4.4 (chain: A, length: 160), 50.0 (chain: B, length: 2)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 160, Sequence coverage: 99.4%

-----120-------130-------140-------150-------160-------170-------180-------190-------200-------210--
GEPKWKKNTLTYRISKYTPSMSSVEVDKAVEMALQAWSSAVPLSFVRINSGEADIMISFENGDHGDSYPFDGPRGTLAHAFAPGEGLGGDTHFDNAEKWT
 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
.EPKWKKNTLTYRISKYTPSMSSVEVDKAVEMALQAWSSAVPLSFVRINSGEADIMISFENGDHGDSYPFDGPRGTLAHAFAPGEGLGGDTHFDNAEKWT

-----220-------230-------240-------250-------260-------270--
MGTNGFNLFTVAAHEFGHALGLAHSTDPSALMYPTYKYKNPYGFHLPKDDVKGIQALYGP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGTNGFNLFTVAAHEFGHALGLAHSTDPSALMYPTYKYKNPYGFHLPKDDVKGIQALYGP

Total number of assignments
- ¹H chemical shifts: 910
- ¹³C chemical shifts: 579
- ¹⁵N chemical shifts: 161

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
123	THR	HG1	5.409
130	THR	HG1	6.762
176	HIS	HD1	11.94
176	HIS	ND1	172.5
176	HIS	NE2	206.5
191	HIS	ND1	177.9
191	HIS	NE2	199.301
203	THR	HG1	2.531
204	HIS	HE2	13.26
204	HIS	ND1	208.86
204	HIS	NE2	170.48
226	HIS	HD1	12.702
226	HIS	ND1	172.9
236	HIS	HD1	13.13
236	HIS	ND1	172.2
236	HIS	NE2	217.0
257	HIS	ND1	172.9
257	HIS	NE2	214.3

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	933	903	96.8
¹³C chemical shifts	719	579	80.5
¹⁵N chemical shifts	164	150	91.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	326	320	98.2
¹³C chemical shifts	320	289	90.3
¹⁵N chemical shifts	149	144	96.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	607	583	96.0
¹³C chemical shifts	399	290	72.7
¹⁵N chemical shifts	15	6	40.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	76	100.0
¹³C chemical shifts	76	75	98.7

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	98	89.9
¹³C chemical shifts	106	1	0.9
¹⁵N chemical shifts	3	0	0.0

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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 160, Sequence coverage: 98.8%
- Total number of restraints: 2780
- Weight of restraints: 1.0 (2780)
- Potential type of restraints: upper-bound-parabolic (2780)
- Range of distance target values: 2.41, 6.15 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
  - Chain_ID: D
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Error
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 160, Sequence coverage: 4.4%
    - Entity_assembly_ID: B, Chain length: 2, Sequence coverage: 50.0%
  - Total number of restraints: 7
  - Weight of restraints: 1.0 (7)
  - Potential type of restraints: upper-bound-parabolic (7)
  - Range of distance target values: 2.8, 2.8 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
    - Chain_ID: D
      None
  - Distance restraints on contact map

Keywords drug discovery, MMP, NMR, protein-ligand interaction, solution structure, MMP-NNGH