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Found 1 Document (0.991 seconds)

BMRB: 19014

2M4N

Solution structure of the putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans

Authors

Harris, R., Hillerich, B., Ahmed, M., Bonanno, J.B., Chamala, S., Evans, B., Lafleur, J., Hammonds, J., Washington, E., Stead, M., Love, J., Attonito, J., Seidel, R.D., Liddington, R.C., Weis, W.I., Nelson, W.J., Girvin, M.E., Almo, S.C.

Assembly

putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans

Entity

1. putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans (polymer, Thiol state: all free), 108 monomers, 11957.32 Da Detail

SMFGGSLKVY GGEIVPTRPY VSILAEINEN ADRILGAALE KYGLEHSKDD FILVEVSNDD DRKSMSDLRE IDGRPIPPTE CPLFEMTARS GNGENGFDSF LAIKRKPH

Formula weight

11957.32 Da

Source organism

Caenorhabditis elegans

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 99.4 %, Completeness (bb): 99.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	99.4 % (1224 of 1231)	99.5 % (641 of 644)	99.6 % (479 of 481)	98.1 % (104 of 106)
Backbone	99.2 % (629 of 634)	99.1 % (217 of 219)	99.7 % (313 of 314)	98.0 % (99 of 101)
Sidechain	99.7 % (693 of 695)	99.8 % (424 of 425)	99.6 % (264 of 265)	100.0 % (5 of 5)
Aromatic	100.0 % (82 of 82)	100.0 % (41 of 41)	100.0 % (41 of 41)
Methyl	100.0 % (106 of 106)	100.0 % (53 of 53)	100.0 % (53 of 53)

1. putative Ras interaction domain of AFD-1 isoform a

SMFGGSLKVY GGEIVPTRPY VSILAEINEN ADRILGAALE KYGLEHSKDD FILVEVSNDD DRKSMSDLRE IDGRPIPPTE CPLFEMTARS GNGENGFDSF LAIKRKPH

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	0.1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	0.1 mM

LACS Plot; CA

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

Referencing offset: -0.05 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.05 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M4N, Strand ID: A Detail

Release date

2013-03-03

Related entities 1. putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans, : 1 : 1 : 5 entities Detail

Experiments performed 12 experiments Detail

1 15N HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	0.1 mM

2 15N NOESY-HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	0.1 mM

3 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	0.1 mM

4 aromatic 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	0.1 mM

5 13C NOESY-HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	0.1 mM

6 13C aromatic NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	0.1 mM

7 HNCO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	0.1 mM

8 HNCACO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	0.1 mM

9 HNCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	0.1 mM

10 HNCOCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	0.1 mM

11 HNCACB

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	0.1 mM

12 CBCACONH

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na Phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	putative Ras interaction domain of AFD-1, isoform a	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	0.1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19014_2m4n.nef
Input source #2: Coordindates	2m4n.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	None
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)

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--------90-------100
SMFGGSLKVYGGEIVPTRPYVSILAEINENADRILGAALEKYGLEHSKDDFILVEVSNDDDRKSMSDLREIDGRPIPPTECPLFEMTARSGNGENGFDSF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMFGGSLKVYGGEIVPTRPYVSILAEINENADRILGAALEKYGLEHSKDDFILVEVSNDDDRKSMSDLREIDGRPIPPTECPLFEMTARSGNGENGFDSF

--------
LAIKRKPH
||||||||
LAIKRKPH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	108	0	0	100.0

Content subtype: combined_19014_2m4n.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1225		100.0 (chain: A, length: 108)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1864 (1)	noe	99.1 (chain: A, length: 108)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	228 (1)	noe	61.1 (chain: A, length: 108)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	119 (119)	.	60.2 (chain: A, length: 108)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 639
  - ¹³C chemical shifts: 478
  - ¹⁵N chemical shifts: 108
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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	644	639	99.2
¹³C chemical shifts	481	478	99.4
¹⁵N chemical shifts	113	108	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	219	215	98.2
¹³C chemical shifts	216	214	99.1
¹⁵N chemical shifts	101	97	96.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	425	424	99.8
¹³C chemical shifts	265	264	99.6
¹⁵N chemical shifts	12	11	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	56	100.0
¹³C chemical shifts	56	56	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	41	100.0
¹³C chemical shifts	41	41	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 99.1%
- Total number of restraints: 1859
- Weight of restraints: 1.0 (1859)
- Potential type of restraints: square-well-parabolic (1859)
- Range of distance target values: 2.4, 4.65 (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: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 61.1%
  - Total number of restraints: 225
  - Weight of restraints: 1.0 (225)
  - Potential type of restraints: square-well-parabolic (225)
  - 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
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 60.2%
- 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
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords New York Structural Genomics Research Consortium, STRUCTURAL GENOMICS, THIOREDOXIN-LIKE, UNKNOWN FUNCTION

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Found 1 Document (0.991 seconds)

BMRB: 19014

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. putative Ras interaction domain of AFD-1, isoform a from Caenorhabditis elegans, : 1 : 1 : 5 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail