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BMRB: 19212

2M7H

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-67NPWNG mutant

Entity

1. rhodostomin 48ARGDWN-67NPWNG mutant (polymer, Thiol state: not reported), 79 monomers, 8743.624 Da Detail

EFHHHHHHGK ECDCSSPENP CCDAATCKLR PGAQCGEGLC CEQCKFSRAG KICRIARGDW NDDRCTGQSA DCPRNPWNG

Formula weight

8743.624 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: 83.6 %, Completeness (bb): 88.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	83.6 % (443 of 530)	83.4 % (373 of 447)	84.3 % (70 of 83)
Backbone	88.1 % (207 of 235)	87.6 % (141 of 161)	89.2 % (66 of 74)
Sidechain	80.0 % (236 of 295)	81.1 % (232 of 286)	44.4 % (4 of 9)
Aromatic	44.4 % (16 of 36)	47.1 % (16 of 34)	0.0 % (0 of 2)
Methyl	100.0 % (16 of 16)	100.0 % (16 of 16)

1. rhodostomin

EFHHHHHHGK ECDCSSPENP CCDAATCKLR PGAQCGEGLC CEQCKFSRAG KICRIARGDW NDDRCTGQSA DCPRNPWNG

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	rhodostomin	natural abundance		2 mM

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
2	rhodostomin	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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
3	rhodostomin	[U-15N]		2 mM

Sample #4

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

#	Name	Isotope labeling	Type	Concentration
4	rhodostomin	[U-15N]		2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2M7H, 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-67NPWNG mutant, : 1 : 9 : 202 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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
1	rhodostomin	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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
1	rhodostomin	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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
2	rhodostomin	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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
2	rhodostomin	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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
3	rhodostomin	[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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
3	rhodostomin	[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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
3	rhodostomin	[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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
3	rhodostomin	[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-67NPWNG mutant

#	Name	Isotope labeling	Type	Concentration
4	rhodostomin	[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_19212_2m7h.nef
Input source #2: Coordindates	2m7h.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	2.023
A:6:CYS:SG	A:14:CYS:SG	unknown	unknown	2.02
A:13:CYS:SG	A:36:CYS:SG	unknown	unknown	2.017
A:27:CYS:SG	A:33:CYS:SG	unknown	unknown	2.023
A:32:CYS:SG	A:57:CYS:SG	unknown	unknown	2.018
A:45:CYS:SG	A:64:CYS:SG	unknown	unknown	2.018

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-
EFHHHHHHGKECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIARGDWNDDRCTGQSADCPRNPWNG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EFHHHHHHGKECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIARGDWNDDRCTGQSADCPRNPWNG
--------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_19212_2m7h.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	439		89.9 (chain: A, length: 79)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	6 (1)	undefined	15.2 (chain: A, length: 79)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	172 (1)	noe	86.1 (chain: A, length: 79)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	9 (1)	hbond	15.2 (chain: A, length: 79)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_7	OK	59 (59)	.	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: 369
  - ¹⁵N chemical shifts: 70
- 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	447	369	82.6
¹⁵N chemical shifts	89	70	78.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	161	144	89.4
¹⁵N chemical shifts	74	66	89.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	286	225	78.7
¹⁵N chemical shifts	15	4	26.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	16	47.1
¹⁵N chemical shifts	2	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- 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_5
  - 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: 172
  - Weight of restraints: 1.0 (172)
  - Potential type of restraints: square-well-parabolic (172)
  - 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_4
    - 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_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 84.8%
- Total number of restraints: 59
- Total number of restraints per polymer type: 59
- Weight of restraints: 1.0 (59)
- Potential type of restraints: square-well-parabolic (59)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Rhodostomin mutant protein

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Found 1 Document (0.71 seconds)

BMRB: 19212

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. rhodostomin 48ARGDWN-67NPWNG mutant, : 1 : 9 : 202 entities Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 6 contents Detail