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Found 1 Document (0.765 seconds)

BMRB: 19211

2M7F

The C-terminal Region of Disintegrin Modulate its 3D Conformation and Cooperate with RGD Loop in Regulating Recognitions of Integrins

Authors

Chuang, W., Chang, Y.

Assembly

rhodostomin 48ARGDWN-67NGLYG mutant

Entity

1. rhodostomin 48ARGDWN-67NGLYG mutant (polymer, Thiol state: not reported), 79 monomers, 8679.580 Da Detail

EFHHHHHHGK ECDCSSPENP CCDAATCKLR PGAQCGEGLC CEQCKFSRAG KICRIARGDW NDDRCTGQSA DCPRNGLYG

Formula weight

8679.58 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS12:SG	1:CYS27:SG
2	disulfide	sing	1:CYS14:SG	1:CYS22:SG
3	disulfide	sing	1:CYS21:SG	1:CYS44:SG
4	disulfide	sing	1:CYS35:SG	1:CYS41:SG
5	disulfide	sing	1:CYS40:SG	1:CYS65:SG
6	disulfide	sing	1:CYS53:SG	1:CYS72:SG

Source organism

Calloselasma rhodostoma

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.9 %, Completeness: 83.0 %, Completeness (bb): 89.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	83.0 % (435 of 524)	82.4 % (364 of 442)	86.6 % (71 of 82)
Backbone	89.5 % (213 of 238)	89.6 % (146 of 163)	89.3 % (67 of 75)
Sidechain	77.6 % (222 of 286)	78.1 % (218 of 279)	57.1 % (4 of 7)
Aromatic	42.4 % (14 of 33)	43.8 % (14 of 32)	0.0 % (0 of 1)
Methyl	100.0 % (18 of 18)	100.0 % (18 of 18)

1. rhodostomin

EFHHHHHHGK ECDCSSPENP CCDAATCKLR PGAQCGEGLC CEQCKFSRAG KICRIARGDW NDDRCTGQSA DCPRNGLYG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
1	Rhodostomin 48ARGDWN-67NGLYG mutant	natural abundance		2 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
2	Rhodostomin 48ARGDWN-67NGLYG mutant	natural abundance		2 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
3	Rhodostomin 48ARGDWN-67NGLYG mutant	[U-15N]		2 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
4	Rhodostomin 48ARGDWN-67NGLYG mutant	[U-15N]		2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2M7F, Strand ID: A Detail

Release date

2013-05-13

Citation

The C-terminal Region of Disintegrin Modulate its 3D Conformation and Cooperate with RGD Loop in Regulating Recognitions of Integrins
Chuang, W., Chang, Y., Shiu, J., Chen, C., Chen, Y.
Not known

Related entities 1. rhodostomin 48ARGDWN-67NGLYG mutant, : 1 : 9 : 209 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
1	Rhodostomin 48ARGDWN-67NGLYG mutant	natural abundance		2 mM

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
1	Rhodostomin 48ARGDWN-67NGLYG mutant	natural abundance		2 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
2	Rhodostomin 48ARGDWN-67NGLYG mutant	natural abundance		2 mM

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
2	Rhodostomin 48ARGDWN-67NGLYG mutant	natural abundance		2 mM

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
3	Rhodostomin 48ARGDWN-67NGLYG mutant	[U-15N]		2 mM

6 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
3	Rhodostomin 48ARGDWN-67NGLYG mutant	[U-15N]		2 mM

7 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
3	Rhodostomin 48ARGDWN-67NGLYG mutant	[U-15N]		2 mM

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
3	Rhodostomin 48ARGDWN-67NGLYG mutant	[U-15N]		2 mM

9 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0, Details 2mM Rhodostomin 48ARGDWN-67NGLYG mutant

#	Name	Isotope labeling	Type	Concentration
4	Rhodostomin 48ARGDWN-67NGLYG mutant	[U-15N]		2 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19211_2m7f.nef
Input source #2: Coordindates	2m7f.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:4:CYS:SG	A:19:CYS:SG	unknown	unknown	2.025
A:6:CYS:SG	A:14:CYS:SG	unknown	unknown	2.021
A:13:CYS:SG	A:36:CYS:SG	unknown	unknown	2.018
A:27:CYS:SG	A:33:CYS:SG	unknown	unknown	2.013
A:32:CYS:SG	A:57:CYS:SG	unknown	unknown	2.017
A:45:CYS:SG	A:64:CYS:SG	unknown	unknown	2.013

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0

Content subtype: combined_19211_2m7f.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	435		89.9 (chain: A, length: 79)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	6 (1)	undefined	15.2 (chain: A, length: 79)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	166 (1)	noe	86.1 (chain: A, length: 79)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	9 (1)	hbond	15.2 (chain: A, length: 79)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	60 (60)	.	84.8 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 89.9%
- Total number of assignments
  - ¹H chemical shifts: 364
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	442	364	82.4
¹⁵N chemical shifts	88	71	80.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	163	146	89.6
¹⁵N chemical shifts	75	67	89.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	279	218	78.1
¹⁵N chemical shifts	13	4	30.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	18	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	14	43.8
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 15.2%
- Total number of restraints: 6
- Weight of restraints: 1.0 (6)
- Potential type of restraints: square-well-parabolic (6)
- Range of distance target values: 2.02, 2.02 (Å)
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 86.1%
  - Total number of restraints: 166
  - Weight of restraints: 1.0 (166)
  - Potential type of restraints: square-well-parabolic (166)
  - Range of distance target values: 2.6, 4.2 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 15.2%
    - Total number of restraints: 9
    - Weight of restraints: 1.0 (9)
    - Potential type of restraints: square-well-parabolic (9)
    - Range of distance target values: 2.0, 2.0 (Å)
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 84.8%
- Total number of restraints: 60
- Total number of restraints per polymer type: 60
- Weight of restraints: 1.0 (60)
- Potential type of restraints: square-well-parabolic (60)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Rhodostomin mutant protein

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Found 1 Document (0.765 seconds)

BMRB: 19211

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. rhodostomin 48ARGDWN-67NGLYG mutant, : 1 : 9 : 209 entities Detail

Experiments performed 9 experiments Detail

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Sample

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NMR combined restraints 6 contents Detail