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BMRB: 19963

2MP5

Structure of Bitistatin_B

Authors

Carbajo, R.J., Calvete, J., Sanz, L., Perez, A.

Assembly

Bitistatin B

Entity

1. Bitistatin B (polymer, Thiol state: all disulfide bound), 83 monomers, 9003.941 Da Detail

SPPVCGNKIL EQGEDCDCGS PANCQDRCCN AATCKLTPGS QCNYGECCDQ CRFKKAGTVC RIARGDWNDD YCTGKSSDCP WNH

Formula weight

9003.941 Da

Entity Connection

disulfide 7 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS5:SG	1:CYS34:SG
2	disulfide	sing	1:CYS16:SG	1:CYS29:SG
3	disulfide	sing	1:CYS18:SG	1:CYS24:SG
4	disulfide	sing	1:CYS28:SG	1:CYS51:SG
5	disulfide	sing	1:CYS42:SG	1:CYS48:SG
6	disulfide	sing	1:CYS47:SG	1:CYS72:SG
7	disulfide	sing	1:CYS60:SG	1:CYS79:SG

Source organism

Bitis arietans

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.1 %, Completeness (bb): 77.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.1 % (718 of 875)	97.8 % (449 of 459)	56.1 % (183 of 326)	95.6 % (86 of 90)
Backbone	77.5 % (378 of 488)	99.4 % (168 of 169)	55.2 % (133 of 241)	98.7 % (77 of 78)
Sidechain	86.1 % (398 of 462)	96.9 % (281 of 290)	67.5 % (108 of 160)	75.0 % (9 of 12)
Aromatic	51.9 % (28 of 54)	96.3 % (26 of 27)	0.0 % (0 of 25)	100.0 % (2 of 2)
Methyl	100.0 % (42 of 42)	100.0 % (21 of 21)	100.0 % (21 of 21)

1. Bitistatin B

SPPVCGNKIL EQGEDCDCGS PANCQDRCCN AATCKLTPGS QCNYGECCDQ CRFKKAGTVC RIARGDWNDD YCTGKSSDCP WNH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5

#	Name	Isotope labeling	Concentration
1	Bitistatin B	[U-99% 2H]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	sodium phosphate	natural abundance	50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 5

#	Name	Isotope labeling	Concentration
5	Bitistatin_B	[U-100% 15N]	1 mM
6	H2O	natural abundance	90 %
7	D2O	[U-99% 2H]	10 %
8	sodium phosphate	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 43 models in PDB: 2MP5, Strand ID: 1 Detail

Release date

2014-11-09

Citation

NMR structure of bitistatin – a missing piece in the evolutionary pathway of snake venom disintegrins
Carbajo, R.J., Calvete, J., Sanz, L., Perez, A.
FEBS J. (2015), 282, 341-360, PubMed 25363287 , DOI 10.1111/febs.13138 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 19947 released on 2014-11-09
Title Structure of Bitistatin_A

Related entities 1. Bitistatin B, : 1 : 2 : 236 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19963_2mp5.nef
Input source #2: Coordindates	2mp5.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)
1:5:CYS:SG	1:34:CYS:SG	unknown, CA 53.1 ppm	unknown	2.031
1:16:CYS:SG	1:29:CYS:SG	unknown, CA 53.9 ppm	unknown	2.033
1:18:CYS:SG	1:24:CYS:SG	oxidized, CA 54.5, CB 47.9 ppm	oxidized, CB 42.6 ppm	2.033
1:28:CYS:SG	1:51:CYS:SG	unknown, CA 52.6 ppm	oxidized, CB 43.2 ppm	2.03
1:42:CYS:SG	1:48:CYS:SG	unknown, CA 53.6 ppm	oxidized, CA 54.7, CB 45.7 ppm	2.031
1:47:CYS:SG	1:72:CYS:SG	oxidized, CA 57.1, CB 41.2 ppm	oxidized, CA 53.4, CB 37.2 ppm	2.027
1:60:CYS:SG	1:79:CYS:SG	oxidized, CA 54.4, CB 43.0 ppm	oxidized, CA 52.0, CB 39.3 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): 1 vs Auth_asym_ID (model): 1

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
1	1	83	0	0	100.0

Content subtype: combined_19963_2mp5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	7		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	723		100.0 (chain: 1, length: 83)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2642 (1)	noe	100.0 (chain: 1, length: 83)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	79 (1)	noe	42.2 (chain: 1, length: 83)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	30 (1)	hbond	26.5 (chain: 1, length: 83)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	82 (82)	.	83.1 (chain: 1, length: 83)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 83, Sequence coverage: 100.0%

--------10--------20--------30--------40--------50--------60--------70--------80---
SPPVCGNKILEQGEDCDCGSPANCQDRCCNAATCKLTPGSQCNYGECCDQCRFKKAGTVCRIARGDWNDDYCTGKSSDCPWNH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SPPVCGNKILEQGEDCDCGSPANCQDRCCNAATCKLTPGSQCNYGECCDQCRFKKAGTVCRIARGDWNDDYCTGKSSDCPWNH

Total number of assignments
- ¹H chemical shifts: 465
- ¹³C chemical shifts: 172
- ¹⁵N chemical shifts: 86

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
35	LYS	HZ1	7.44
35	LYS	HZ2	7.44
35	LYS	HZ3	7.44
52	ARG	HH11	6.6
52	ARG	HH12	6.6
52	ARG	HH21	6.6
52	ARG	HH22	6.6
54	LYS	HZ1	7.69
54	LYS	HZ2	7.69
54	LYS	HZ3	7.69
61	ARG	HH11	5.98
61	ARG	HH12	5.98
61	ARG	HH21	5.98
61	ARG	HH22	5.98
75	LYS	HZ1	7.59
75	LYS	HZ2	7.59
75	LYS	HZ3	7.59

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	459	448	97.6
¹³C chemical shifts	326	172	52.8
¹⁵N chemical shifts	94	86	91.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	169	167	98.8
¹³C chemical shifts	166	67	40.4
¹⁵N chemical shifts	78	77	98.7

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	290	281	96.9
¹³C chemical shifts	160	105	65.6
¹⁵N chemical shifts	16	9	56.2

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	21	100.0
¹³C chemical shifts	21	21	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	26	96.3
¹³C chemical shifts	25	0	0.0
¹⁵N chemical shifts	2	2	100.0

Redox state of CYS
Peptide bond of PRO
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: 1

Covalent bonds

Saveframe: assembly
- Status: OK
- Total number of restraints: 7
- Covelent bonds on contact map

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 83, Sequence coverage: 100.0%
- Total number of restraints: 2642
- Weight of restraints: 1.0 (2642)
- Potential type of restraints: square-well-parabolic (2642)
- Range of distance target values: 1.1, 3.25 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: 1
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: 1, Chain length: 83, Sequence coverage: 42.2%
  - Total number of restraints: 78
  - Weight of restraints: 1.0 (78)
  - Potential type of restraints: square-well-parabolic (78)
  - Range of distance target values: 2.5, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: 1
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: 1, Chain length: 83, Sequence coverage: 26.5%
    - Total number of restraints: 30
    - Weight of restraints: 1.0 (30)
    - Potential type of restraints: square-well-parabolic (30)
    - Range of distance target values: 1.15, 2.9 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: 1
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 83, Sequence coverage: 83.1%
- Total number of restraints: 82
- Total number of restraints per polymer type: 82
- Weight of restraints: 1.0 (82)
- Potential type of restraints: square-well-parabolic (82)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: 1

Keywords Bitis arietans, snake venom, disintegrin, NMR

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Found 1 Document (0.764 seconds)

BMRB: 19963

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Bitistatin B, : 1 : 2 : 236 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

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NMR combined restraints 6 contents Detail