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BMRB: 17963

2LJV

Solution structure of Rhodostomin G50L mutant

Authors

Chuang, W., Shiu, J., Chen, C., Chen, Y., Chang, Y., Chang, Y., Huang, C.

Assembly

Rhodostomin G50L mutant

Entity

1. Rhodostomin G50L mutant (polymer, Thiol state: all disulfide bound), 68 monomers, 7386.376 Da Detail

GKECDCSSPE NPCCDAATCK LRPGAQCGEG LCCEQCKFSR AGKICRIPRL DMPDDRCTGQ SADCPRYH

Formula weight

7386.376 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS19:SG
2	disulfide	sing	1:CYS6:SG	1:CYS14:SG
3	disulfide	sing	1:CYS13:SG	1:CYS36:SG
4	disulfide	sing	1:CYS27:SG	1:CYS33:SG
5	disulfide	sing	1:CYS32:SG	1:CYS57:SG
6	disulfide	sing	1:CYS45:SG	1:CYS64: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: 100.0 %, Completeness: 94.9 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	94.9 % (427 of 450)	94.0 % (361 of 384)	100.0 % (66 of 66)
Backbone	100.0 % (198 of 198)	100.0 % (136 of 136)	100.0 % (62 of 62)
Sidechain	90.9 % (229 of 252)	90.7 % (225 of 248)	100.0 % (4 of 4)
Aromatic	72.7 % (8 of 11)	72.7 % (8 of 11)
Methyl	100.0 % (17 of 17)	100.0 % (17 of 17)

1. Rhodostomin G50L mutant

GKECDCSSPE NPCCDAATCK LRPGAQCGEG LCCEQCKFSR AGKICRIPRL DMPDDRCTGQ SADCPRYH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	Rhodostomin G50L mutant	natural abundance	2 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
4	Rhodostomin G50L mutant	natural abundance		2 mM
5	D2O	natural abundance		100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0

#	Name	Isotope labeling	Concentration
6	Rhodostomin G50L mutant	[U-99% 15N]	2 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 300 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
9	Rhodostomin G50L mutant	[U-99% 15N]		2 mM
10	D2O	natural abundance		100 %

Protein Blocks Logo

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

Release date

2012-09-30

Citation

Design of Integrin AlphaVbeta3-Specific Disintegrin for Cancer Therapy
Shiu, J., Chen, C., Chen, Y., Chang, Y.
Not known

Related entities 1. Rhodostomin G50L mutant, : 1 : 15 : 221 entities Detail

Experiments performed 9 experiments Detail

1 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

#	Name	Isotope labeling	Concentration
6	Rhodostomin G50L mutant	[U-99% 15N]	2 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 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

#	Name	Isotope labeling	Concentration
6	Rhodostomin G50L mutant	[U-99% 15N]	2 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 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

#	Name	Isotope labeling	Concentration
6	Rhodostomin G50L mutant	[U-99% 15N]	2 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

4 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

#	Name	Isotope labeling	Concentration
6	Rhodostomin G50L mutant	[U-99% 15N]	2 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 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

#	Name	Isotope labeling	Type	Concentration
9	Rhodostomin G50L mutant	[U-99% 15N]		2 mM
10	D2O	natural abundance		100 %

6 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

#	Name	Isotope labeling	Concentration
1	Rhodostomin G50L mutant	natural abundance	2 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

7 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

#	Name	Isotope labeling	Concentration
1	Rhodostomin G50L mutant	natural abundance	2 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 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

#	Name	Isotope labeling	Type	Concentration
4	Rhodostomin G50L mutant	natural abundance		2 mM
5	D2O	natural abundance		100 %

9 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

#	Name	Isotope labeling	Type	Concentration
4	Rhodostomin G50L mutant	natural abundance		2 mM
5	D2O	natural abundance		100 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17963_2ljv.nef
Input source #2: Coordindates	2ljv.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	2.021
A:6:CYS:SG	A:14:CYS:SG	unknown	unknown	2.02
A:13:CYS:SG	A:36:CYS:SG	unknown	unknown	2.019
A:27:CYS:SG	A:33:CYS:SG	unknown	unknown	2.012
A:32:CYS:SG	A:57:CYS:SG	unknown	unknown	2.02
A:45:CYS:SG	A:64:CYS:SG	unknown	unknown	2.017

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--------
GKECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIPRLDMPDDRCTGQSADCPRYH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GKECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIPRLDMPDDRCTGQSADCPRYH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	68	0	0	100.0

Content subtype: combined_17963_2ljv.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	Warning	423		100.0 (chain: A, length: 68)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1045 (1)	noe	100.0 (chain: A, length: 68)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	6 (1)	disulfide_bond	17.6 (chain: A, length: 68)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	153 (1)	noe	94.1 (chain: A, length: 68)
4	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	10 (1)	hbond	17.6 (chain: A, length: 68)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	55 (55)	.	94.1 (chain: A, length: 68)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 356
  - ¹⁵N chemical shifts: 67
- 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	384	355	92.4
¹⁵N chemical shifts	72	67	93.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	136	134	98.5
¹⁵N chemical shifts	62	62	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	248	221	89.1
¹⁵N chemical shifts	10	5	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	17	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	8	72.7

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 100.0%
- Total number of restraints: 1045
- Weight of restraints: 1.0 (1045)
- Potential type of restraints: square-well-parabolic (1045)
- Range of distance target values: 2.6, 5.35 (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_3
  - Status: OK
  - Experiment type: disulfide_bond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 17.6%
  - 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: 68, Sequence coverage: 94.1%
    - Total number of restraints: 153
    - Weight of restraints: 1.0 (153)
    - Potential type of restraints: square-well-parabolic (153)
    - 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: 68, Sequence coverage: 17.6%
      - Total number of restraints: 10
        Total hydrogen bond restraints: 10
        O...H-x: 4
        Long range: 6
        O...H-x: 6
      - Weight of restraints: 1.0 (10)
        Total hydrogen bond restraints: 1.0 (10)
        O...H-x: 1.0 (4)
        Long range: 1.0 (6)
        O...H-x: 1.0 (6)
      - Potential type of restraints: square-well-parabolic (10)
        Total hydrogen bond restraints: square-well-parabolic (10)
        O...H-x: square-well-parabolic (4)
        Long range: square-well-parabolic (6)
        O...H-x: square-well-parabolic (6)
      - 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_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 94.1%
- Total number of restraints: 55
- Total number of restraints per polymer type: 55
- Weight of restraints: 1.0 (55)
- Potential type of restraints: square-well-parabolic (55)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords disintegrin, integrin, NMR, RGD

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Found 1 Document (0.72 seconds)

BMRB: 17963

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. Rhodostomin G50L mutant, : 1 : 15 : 221 entities Detail

Experiments performed 9 experiments Detail

Instrument

Sample

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Sample

Instrument

Sample

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Sample

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NMR combined restraints 7 contents Detail