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BMRB: 18182

2LNW

Identification and structural basis for a novel interaction between Vav2 and Arap3

Authors

Wu, B., Zhang, J., Wu, J., Shi, Y.

Assembly

Vav2 and Arap3

Entity

1. Vav2 and Arap3, entity 1 (polymer, Thiol state: all free), 113 monomers, 13458.01 Da Detail

SRPPSREIDY TAYPWFAGNM ERQQTDNLLK SHASGTYLIR ERPAEAERFA ISIKFNDEVK HIKVVEKDNW IHITEAKKFD SLLELVEYYQ CHSLKESFKQ LDTTLKYPYK SRE

2. Vav2 and Arap3, entity 2 (polymer, Thiol state: not present), 9 monomers, 1130.051 Da Detail

EEPVXEEVG

Total weight

14588.061 Da

Max. entity weight

13458.01 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 90.3 %, Completeness (bb): 92.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.3 % (1338 of 1482)	96.9 % (755 of 779)	81.7 % (472 of 578)	88.8 % (111 of 125)
Backbone	92.9 % (663 of 714)	94.6 % (226 of 239)	91.7 % (330 of 360)	93.0 % (107 of 115)
Sidechain	88.4 % (783 of 886)	98.0 % (529 of 540)	74.4 % (250 of 336)	40.0 % (4 of 10)
Aromatic	58.9 % (86 of 146)	98.6 % (72 of 73)	19.7 % (14 of 71)	0.0 % (0 of 2)
Methyl	96.5 % (110 of 114)	100.0 % (57 of 57)	93.0 % (53 of 57)

1. entity 1

SRPPSREIDY TAYPWFAGNM ERQQTDNLLK SHASGTYLIR ERPAEAERFA ISIKFNDEVK HIKVVEKDNW IHITEAKKFD SLLELVEYYQ CHSLKESFKQ LDTTLKYPYK SRE

2. entity 2

EEPVXEEVG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]		1 mM
11	entity_2	natural abundance		3 mM
12	potassium phosphate	natural abundance		5 mM
13	sodium chloride	natural abundance		75 mM
14	DTT	natural abundance		5 mM
15	EDTA	natural abundance		2 mM
16	sodium phosphate	natural abundance		20 mM
17	D2O	natural abundance		100 %

Protein Blocks Logo

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

Release date

2012-11-18

Citation

Identification and structural basis for a novel interaction between Vav2 and Arap3
Wu, B., Wang, F., Zhang, J., Zhang, Z., Qin, L., Peng, J., Li, F., Liu, J., Lu, G., Gong, Q., Yao, X., Wu, J., Shi, Y.
J. Struct. Biol. (2012), 180, 84-95, PubMed 22750419 , DOI 10.1016/j.jsb.2012.06.011 , Abstract

Related entities 1. Vav2 and Arap3, entity 1, : 2 : 182 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

5 3D HCACO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

6 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

7 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

8 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

9 3D H(CCO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1 mM
2	entity_2	natural abundance		3 mM
3	potassium phosphate	natural abundance		5 mM
4	sodium phosphate	natural abundance		20 mM
5	DTT	natural abundance		5 mM
6	EDTA	natural abundance		2 mM
7	sodium chloride	natural abundance		75 mM
8	H2O	natural abundance		90 %
9	D2O	natural abundance		10 %

10 3D HCCH-TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]		1 mM
11	entity_2	natural abundance		3 mM
12	potassium phosphate	natural abundance		5 mM
13	sodium chloride	natural abundance		75 mM
14	DTT	natural abundance		5 mM
15	EDTA	natural abundance		2 mM
16	sodium phosphate	natural abundance		20 mM
17	D2O	natural abundance		100 %

11 3D HCCH-COSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]		1 mM
11	entity_2	natural abundance		3 mM
12	potassium phosphate	natural abundance		5 mM
13	sodium chloride	natural abundance		75 mM
14	DTT	natural abundance		5 mM
15	EDTA	natural abundance		2 mM
16	sodium phosphate	natural abundance		20 mM
17	D2O	natural abundance		100 %

12 3D 1H-13C NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
10	entity_1	[U-100% 13C; U-100% 15N]		1 mM
11	entity_2	natural abundance		3 mM
12	potassium phosphate	natural abundance		5 mM
13	sodium chloride	natural abundance		75 mM
14	DTT	natural abundance		5 mM
15	EDTA	natural abundance		2 mM
16	sodium phosphate	natural abundance		20 mM
17	D2O	natural abundance		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18182_2lnw.nef
Input source #2: Coordindates	2lnw.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:4:VAL:C	2:5:PTR:N	unknown	unknown	n/a
2:5:PTR:C	2:6:GLU:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1408	PTR	O-PHOSPHOTYROSINE	Assigned chemical shifts, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

650-----660-------670-------680-------690-------700-------710-------720-------730-------740-------75
MGHHHHHHMSRPPSREIDYTAYPWFAGNMERQQTDNLLKSHASGTYLIRERPAEAERFAISIKFNDEVKHIKVVEKDNWIHITEAKKFDSLLELVEYYQC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHMSRPPSREIDYTAYPWFAGNMERQQTDNLLKSHASGTYLIRERPAEAERFAISIKFNDEVKHIKVVEKDNWIHITEAKKFDSLLELVEYYQC
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------760-------770-
HSLKESFKQLDTTLKYPYKSRE
||||||||||||||||||||||
HSLKESFKQLDTTLKYPYKSRE
-------110-------120--

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

---1410--
EEPVXEEVG
|||||||||
EEPVXEEVG
---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	122	0	0	100.0
B	B	9	0	0	100.0

Content subtype: combined_18182_2lnw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1334		92.6 (chain: A, length: 122), 77.8 (chain: B, length: 9)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2122 (1)	noe	90.2 (chain: A, length: 122), 22.2 (chain: B, length: 9)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	46 (1)	hbond	27.9 (chain: A, length: 122)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	119 (119)	.	71.3 (chain: A, length: 122)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 92.6%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 77.8%
- Total number of assignments
  - ¹H chemical shifts: 768
  - ¹³C chemical shifts: 455
  - ¹⁵N chemical shifts: 111
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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: A
  - Chain_ID: B

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 90.2%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 22.2%
- Total number of restraints: 2122
- Weight of restraints: 1.0 (2122)
- Potential type of restraints: square-well-parabolic (2122)
- Range of distance target values: 2.4, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 122, Sequence coverage: 27.9%
  - Total number of restraints: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: square-well-parabolic (46)
  - Range of distance target values: 1.95, 2.95 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 71.3%
- Total number of restraints: 119
- Total number of restraints per polymer type: 119
- Weight of restraints: 1.0 (119)
- Potential type of restraints: square-well-parabolic (119)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Identification and structural basis for a novel interaction between Vav2 and Arap3