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Found 1 Document (1.029 seconds)

BMRB: 18843

2M74

1H, 13C and 15N assignments of the four N-terminal domains of human fibrillin-1

Authors

Yadin, D.A., Robertson, I.B., Jensen, S.A., Handford, P.A., Redfield, C.

Assembly

FUN-EGF3

Entity

1. FUN-EGF3 (polymer, Thiol state: all disulfide bound), 136 monomers, 14103.94 Da Detail

SARGGGGHDA LKGPNVCGSR YNAYCCPGWK TLPGGNQCIV PICRHSCGDG FCSRPNMCTC PSGQIAPSCG SRSIQHCNIR CMNGGSCSDD HCLCQKGYIG THCGQPVCES GCLNGGRCVA PNRCACTYGF TGPQCE

Formula weight

14103.94 Da

Entity Connection

disulfide 11 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS17:SG	1:CYS26:SG
2	disulfide	sing	1:CYS25:SG	1:CYS38:SG
3	disulfide	sing	1:CYS43:SG	1:CYS52:SG
4	disulfide	sing	1:CYS47:SG	1:CYS58:SG
5	disulfide	sing	1:CYS60:SG	1:CYS69:SG
6	disulfide	sing	1:CYS77:SG	1:CYS87:SG
7	disulfide	sing	1:CYS81:SG	1:CYS92:SG
8	disulfide	sing	1:CYS94:SG	1:CYS103:SG
9	disulfide	sing	1:CYS108:SG	1:CYS118:SG
10	disulfide	sing	1:CYS112:SG	1:CYS124:SG
11	disulfide	sing	1:CYS126:SG	1:CYS135:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 96.3 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.3 % (1345 of 1396)	96.0 % (700 of 729)	96.8 % (509 of 526)	96.5 % (136 of 141)
Backbone	97.5 % (776 of 796)	97.2 % (277 of 285)	98.2 % (378 of 385)	96.0 % (121 of 126)
Sidechain	94.2 % (672 of 713)	94.1 % (418 of 444)	94.1 % (239 of 254)	100.0 % (15 of 15)
Aromatic	77.4 % (65 of 84)	78.6 % (33 of 42)	75.6 % (31 of 41)	100.0 % (1 of 1)
Methyl	94.9 % (74 of 78)	94.9 % (37 of 39)	94.9 % (37 of 39)

1. FUN-EGF3

SARGGGGHDA LKGPNVCGSR YNAYCCPGWK TLPGGNQCIV PICRHSCGDG FCSRPNMCTC PSGQIAPSCG SRSIQHCNIR CMNGGSCSDD HCLCQKGYIG THCGQPVCES GCLNGGRCVA PNRCACTYGF TGPQCE

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
1	FUN-EGF3	[U-99% 15N]		1.5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
2	FUN-EGF3	[U-99% 15N]		0.5 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
3	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
4	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.75 ppm	internal	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	4.75 ppm	internal	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.75 ppm	internal	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	4.75 ppm	internal	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.75 ppm	internal	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	4.75 ppm	internal	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.75 ppm	internal	indirect	0.2514495
¹H	water	protons	4.75 ppm	internal	direct	1.0
¹⁵N	water	protons	4.75 ppm	internal	indirect	0.1013291

Referencing offset: 0.58 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M74, Strand ID: A Detail

Release date

2013-01-28

Citation

¹H, ¹³C and ¹⁵N assignments of the four N-terminal domains of human fibrillin-1
Yadin, D.A., Robertson, I.B., Jensen, S.A., Handford, P.A., Redfield, C.
Biomol. NMR Assign. (2014), 8, 75-80, PubMed 23264024 , DOI 10.1007/s12104-012-9456-0 , Abstract

Related entities 1. FUN-EGF3, : 1 : 2 : 130 entities Detail

Interaction partners 1. FUN-EGF3, : 23 interactors Detail

More details for 23 interactors identified by 11 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
1	FUN-EGF3	[U-99% 15N]		1.5 mM

2 3D 1H-15N NOESY

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
1	FUN-EGF3	[U-99% 15N]		1.5 mM

3 3D 1H-15N TOCSY

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
1	FUN-EGF3	[U-99% 15N]		1.5 mM

4 2D 1H-1H TOCSY

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
2	FUN-EGF3	[U-99% 15N]		0.5 mM

5 2D DQF-COSY

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
2	FUN-EGF3	[U-99% 15N]		0.5 mM

6 2D 1H-1H NOESY

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
2	FUN-EGF3	[U-99% 15N]		0.5 mM

7 3D HNCA

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
3	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

8 3D (H)CC(CO)NH

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
3	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

9 3D HNCO

Instrument

Bruker Avance - 500 MHz with TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
3	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

10 3D HN(CA)CO

Instrument

Bruker Avance - 500 MHz with TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
3	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

11 2D 1H-13C HSQC aliphatic

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
4	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

12 3D HCCH-TOCSY

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
4	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

13 3D 1H-13C NOESY aliphatic

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
4	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

14 2D 1H-13C HSQC aromatic

Instrument

Home-built home-built using GE Omega software - 600 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
4	FUN-EGF3	[U-99% 13C; U-99% 15N]		1.5 mM

15 3D 1H-15N HSQC-NOESY-HSQC

Instrument

Home-built home-built using GE Omega software - 750 MHz home-built spectrometer with triple-axis gradient probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.40

#	Name	Isotope labeling	Type	Concentration
1	FUN-EGF3	[U-99% 15N]		1.5 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_18843_2m74.nef
Input source #2: Coordindates	2m74.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:59:CYS:SG	A:68:CYS:SG	oxidized, CA 59.526, CB 41.436 ppm	oxidized, CA 53.737, CB 39.704 ppm	2.018
A:67:CYS:SG	A:80:CYS:SG	oxidized, CA 53.025, CB 35.626 ppm	oxidized, CA 55.097, CB 38.503 ppm	2.019
A:85:CYS:SG	A:94:CYS:SG	oxidized, CA 59.167, CB 39.104 ppm	oxidized, CA 57.114, CB 40.224 ppm	2.017
A:89:CYS:SG	A:100:CYS:SG	oxidized, CA 53.508, CB 36.656 ppm	oxidized, CA 52.76, CB 41.729 ppm	2.021
A:102:CYS:SG	A:111:CYS:SG	oxidized, CA 52.402, CB 35.886 ppm	oxidized, CA 53.079, CB 39.588 ppm	2.014
A:119:CYS:SG	A:129:CYS:SG	oxidized, CA 56.452, CB 41.693 ppm	oxidized, CA 56.255, CB 41.952 ppm	2.016
A:123:CYS:SG	A:134:CYS:SG	oxidized, CA 53.18, CB 39.566 ppm	oxidized, CA 55.033, CB 41.933 ppm	2.022
A:136:CYS:SG	A:145:CYS:SG	oxidized, CA 53.161, CB 37.407 ppm	oxidized, CA 54.921, CB 36.362 ppm	2.019
A:150:CYS:SG	A:160:CYS:SG	oxidized, CA 58.959, CB 37.184 ppm	oxidized, CA 56.616, CB 39.133 ppm	2.018
A:154:CYS:SG	A:166:CYS:SG	oxidized, CA 53.15, CB 38.943 ppm	oxidized, CA 54.141, CB 43.034 ppm	2.021
A:168:CYS:SG	A:177:CYS:SG	oxidized, CA 53.461, CB 39.146 ppm	unknown, CA 54.07 ppm	2.028

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

------50--------60--------70--------80--------90-------100-------110-------120-------130-------140--
SARGGGGHDALKGPNVCGSRYNAYCCPGWKTLPGGNQCIVPICRHSCGDGFCSRPNMCTCPSGQIAPSCGSRSIQHCNIRCMNGGSCSDDHCLCQKGYIG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SARGGGGHDALKGPNVCGSRYNAYCCPGWKTLPGGNQCIVPICRHSCGDGFCSRPNMCTCPSGQIAPSCGSRSIQHCNIRCMNGGSCSDDHCLCQKGYIG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----150-------160-------170--------
THCGQPVCESGCLNGGRCVAPNRCACTYGFTGPQCE
||||||||||||||||||||||||||||||||||||
THCGQPVCESGCLNGGRCVAPNRCACTYGFTGPQCE
-------110-------120-------130------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	136	0	0	100.0

Content subtype: combined_18843_2m74.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	11		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1353		99.3 (chain: A, length: 136)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1093 (1)	noe	79.4 (chain: A, length: 136)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	3011 (1)	noe	87.5 (chain: A, length: 136)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	137 (137)	.	83.1 (chain: A, length: 136)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	54 (54)	.	39.7 (chain: A, length: 136)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 99.3%
- Total number of assignments
  - ¹H chemical shifts: 705
  - ¹³C chemical shifts: 512
  - ¹⁵N chemical shifts: 136
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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	729	705	96.7
¹³C chemical shifts	526	512	97.3
¹⁵N chemical shifts	149	136	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	285	280	98.2
¹³C chemical shifts	272	270	99.3
¹⁵N chemical shifts	126	121	96.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	444	425	95.7
¹³C chemical shifts	254	242	95.3
¹⁵N chemical shifts	23	15	65.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	41	100.0
¹³C chemical shifts	41	41	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	35	83.3
¹³C chemical shifts	41	31	75.6
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 79.4%
- Total number of restraints: 1093
- Weight of restraints: 1.0 (1093)
- Potential type of restraints: square-well-parabolic (1093)
- Range of distance target values: 1.4, 3.25 (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_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 87.5%
  - Total number of restraints: 3006
  - Weight of restraints: 1.0 (3006)
  - Potential type of restraints: square-well-parabolic (3006)
  - Range of distance target values: 1.4, 4.0 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 83.1%
- Total number of restraints: 137
- Total number of restraints per polymer type: 137
- Weight of restraints: 1.0 (137)
- Potential type of restraints: square-well-parabolic (137)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 39.7%
- Total number of restraints: 54
- Potential type of restraints: undefined (54)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords extracellular matrix, Human fibrillin-1 N-terminus, microfibril, NMR resonance assignments

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Found 1 Document (1.029 seconds)

BMRB: 18843

Sample #1

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Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. FUN-EGF3, : 1 : 2 : 130 entities Detail

Interaction partners 1. FUN-EGF3, : 23 interactors Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 6 contents Detail