BMRBj - BMREntryMaster

Found 1 Document (0.684 seconds)

BMRB: 15477

2JVE

Solution structure of the extracellular domain of Prod1, a protein implicated in proximodistal identity during amphibian limb regeneration

Authors

Garza-Garcia, A., Harris, R., Esposito, D., Driscoll, P.C.

Assembly

Prod1

Entity

1. Prod1 (polymer, Thiol state: free and disulfide bound), 91 monomers, 10208.37 Da Detail

MGSSHHHHHH SSGLVPRGSH MALKCFTRNG DDRTVTTCAE EQTRCLFVQL PYSEIQECKT VQQCAEVLEE VTAIGYPAKC CCEDLCNRSE Q

Formula weight

10208.37 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS25:SG	1:CYS45:SG
2	disulfide	sing	1:CYS38:SG	1:CYS58:SG
3	disulfide	sing	1:CYS64:SG	1:CYS80:SG
4	disulfide	sing	1:CYS81:SG	1:CYS86:SG

Source organism

Notophthalmus viridescens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 79.1 %, Completeness: 76.8 %, Completeness (bb): 78.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.8 % (770 of 1003)	75.6 % (393 of 520)	78.8 % (305 of 387)	75.0 % (72 of 96)
Backbone	78.9 % (426 of 540)	77.2 % (142 of 184)	79.9 % (214 of 268)	79.5 % (70 of 88)
Sidechain	75.4 % (414 of 549)	74.7 % (251 of 336)	78.5 % (161 of 205)	25.0 % (2 of 8)
Aromatic	43.8 % (28 of 64)	43.8 % (14 of 32)	43.8 % (14 of 32)
Methyl	87.5 % (70 of 80)	87.5 % (35 of 40)	87.5 % (35 of 40)

1. Prod1

MGSSHHHHHH SSGLVPRGSH MALKCFTRNG DDRTVTTCAE EQTRCLFVQL PYSEIQECKT VQQCAEVLEE VTAIGYPAKC CCEDLCNRSE Q

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Prod1	[U-15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	EDTA	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Prod1	[U-13C; U-15N]	1 mM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	Prod1	[U-13C; U-15N]	1 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	EDTA	natural abundance	1 mM
17	D2O		100 %

LACS Plot; CA

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

Referencing offset: 0.25 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.25 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.04 ppm, Outliers: 3 Detail

LACS Plot; CO

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

Referencing offset: 0.02 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2009-10-13

Citation

Solution structure and phylogenetics of Prod1, a member of the three-finger protein superfamily implicated in salamander limb regeneration
Garza-Garcia, A., Harris, R., Esposito, D., Gates, P.B., Driscoll, P.C.
PLoS One (2009), 4, e7123-e7123, PubMed 19771161 , DOI 10.1371/journal.pone.0007123 , Abstract

Related entities 1. Prod1, : 1 : 8 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Prod1	[U-15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	EDTA	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	Prod1	[U-13C; U-15N]	1 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	EDTA	natural abundance	1 mM
17	D2O		100 %

3 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Prod1	[U-15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	EDTA	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

4 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	Prod1	[U-13C; U-15N]	1 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	EDTA	natural abundance	1 mM
17	D2O		100 %

5 3D 1H-13C aromatic NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	Prod1	[U-13C; U-15N]	1 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	EDTA	natural abundance	1 mM
17	D2O		100 %

6 3D CBCA(CO)NH

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Prod1	[U-13C; U-15N]	1 mM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

7 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Prod1	[U-13C; U-15N]	1 mM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

8 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Prod1	[U-13C; U-15N]	1 mM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

9 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Prod1	[U-13C; U-15N]	1 mM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

10 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Prod1	[U-13C; U-15N]	1 mM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

11 3D HN(CA)CO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Prod1	[U-13C; U-15N]	1 mM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

12 3D HA(CA)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Prod1	[U-13C; U-15N]	1 mM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

13 3D HN(CACO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	Prod1	[U-13C; U-15N]	1 mM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	150 mM
10	EDTA	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

14 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	Prod1	[U-13C; U-15N]	1 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	EDTA	natural abundance	1 mM
17	D2O		100 %

15 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
13	Prod1	[U-13C; U-15N]	1 mM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	150 mM
16	EDTA	natural abundance	1 mM
17	D2O		100 %

16 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Prod1	[U-15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	150 mM
4	EDTA	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15477_2jve.nef
Input source #2: Coordindates	2jve.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:22:CYS:SG	A:42:CYS:SG	oxidized, CA 51.68, CB 41.829 ppm	oxidized, CA 51.956, CB 38.526 ppm	2.03
A:35:CYS:SG	A:55:CYS:SG	oxidized, CA 52.962, CB 37.439 ppm	oxidized, CA 57.749, CB 45.523 ppm	2.026
A:61:CYS:SG	A:77:CYS:SG	oxidized, CA 64.735, CB 40.828 ppm	oxidized, CA 56.029, CB 47.796 ppm	2.025
A:78:CYS:SG	A:83:CYS:SG	oxidized, CA 54.237, CB 47.557 ppm	oxidized, CA 57.206, CB 47.155 ppm	2.029

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--------80--------
MGSSHHHHHHSSGLVPRGSHMALKCFTRNGDDRTVTTCAEEQTRCLFVQLPYSEIQECKTVQQCAEVLEEVTAIGYPAKCCCEDLCNRSEQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMALKCFTRNGDDRTVTTCAEEQTRCLFVQLPYSEIQECKTVQQCAEVLEEVTAIGYPAKCCCEDLCNRSEQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	91	0	0	100.0

Content subtype: combined_15477_2jve.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	758		78.0 (chain: A, length: 91)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1244 (1)	noe	78.0 (chain: A, length: 91)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	23 (1)	noe	11.0 (chain: A, length: 91)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	12 (1)	undefined	8.8 (chain: A, length: 91)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	18 (1)	hbond	14.3 (chain: A, length: 91)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	88 (88)	.	62.6 (chain: A, length: 91)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 78.0%
- Total number of assignments
  - ¹H chemical shifts: 389
  - ¹³C chemical shifts: 300
  - ¹⁵N chemical shifts: 69
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	520	389	74.8
¹³C chemical shifts	387	300	77.5
¹⁵N chemical shifts	101	69	68.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	184	142	77.2
¹³C chemical shifts	182	142	78.0
¹⁵N chemical shifts	88	69	78.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	336	247	73.5
¹³C chemical shifts	205	158	77.1
¹⁵N chemical shifts	13	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	36	85.7
¹³C chemical shifts	42	36	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	14	43.8
¹³C chemical shifts	32	14	43.8

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: 91, Sequence coverage: 78.0%
- Total number of restraints: 1242
- Weight of restraints: 1.0 (1242)
- Potential type of restraints: square-well-parabolic (1242)
- Range of distance target values: 2.0, 3.9 (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: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 11.0%
  - Total number of restraints: 23
  - Weight of restraints: 1.0 (23)
  - Potential type of restraints: square-well-parabolic (23)
  - Range of distance target values: 3.4, 3.65 (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: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 8.8%
    - Total number of restraints: 12
    - Weight of restraints: 1.0 (12)
    - Potential type of restraints: square-well-parabolic (12)
    - Range of distance target values: 2.05, 3.05 (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: 91, Sequence coverage: 14.3%
      - Total number of restraints: 18
        Total hydrogen bond restraints: 18
        O...h-N: 9
        O...H-x: 9
      - Weight of restraints: 1.0 (18)
        Total hydrogen bond restraints: 1.0 (18)
        O...h-N: 1.0 (9)
        O...H-x: 1.0 (9)
      - Potential type of restraints: square-well-parabolic (18)
        Total hydrogen bond restraints: square-well-parabolic (18)
        O...h-N: square-well-parabolic (9)
        O...H-x: square-well-parabolic (9)
      - Range of distance target values: 2.05, 3.05 (Å)
      - Histogram of distance target values
      - 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: 91, Sequence coverage: 62.6%
- Total number of restraints: 88
- Total number of restraints per polymer type: 88
- Weight of restraints: 1.0 (88)
- Potential type of restraints: square-well-parabolic (88)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CD59, Limb regeneration, Ly-6, three-finger snake toxin, UPAR

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Found 1 Document (0.684 seconds)

BMRB: 15477

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Prod1, : 1 : 8 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 7 contents Detail