BMRBj - BMREntryMaster

Found 1 Document (1.124 seconds)

BMRB: 18178

2LNS

Solution structure of AGR2 residues 41-175

Authors

Patel, P., Clarke, C.J., Barraclough, D.L., Rudland, P.S., Barraclough, R., Lian, L.

Assembly

AGR2 residues 41-175

Entity

1. AGR2 residues 41-175 (polymer, Thiol state: all free), 140 monomers, 16167.40 × 2 Da Detail

IDPFTPQTLS RGWGDQLIWT QTYEEALYKS KTSNKPLMII HHLDECPHSQ ALKKVFAENK EIQKLAEQFV LLNLVYETTD KHLSPDGQYV PRIMFVDPSL TVRADITGRY SNRLYAYEPA DTALLLDNMK KALKLLKTEL

Total weight

32334.8 Da

Max. entity weight

16167.4 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 51.5 %, Completeness (bb): 80.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	51.5 % (877 of 1704)	28.5 % (253 of 888)	72.8 % (488 of 670)	93.2 % (136 of 146)
Backbone	80.9 % (667 of 824)	50.4 % (139 of 276)	96.2 % (400 of 416)	97.0 % (128 of 132)
Sidechain	33.5 % (340 of 1016)	18.6 % (114 of 612)	55.9 % (218 of 390)	57.1 % (8 of 14)
Aromatic	0.0 % (0 of 136)	0.0 % (0 of 68)	0.0 % (0 of 66)	0.0 % (0 of 2)
Methyl	75.0 % (129 of 172)	67.4 % (58 of 86)	82.6 % (71 of 86)

1. AGR2

IDPFTPQTLS RGWGDQLIWT QTYEEALYKS KTSNKPLMII HHLDECPHSQ ALKKVFAENK EIQKLAEQFV LLNLVYETTD KHLSPDGQYV PRIMFVDPSL TVRADITGRY SNRLYAYEPA DTALLLDNMK KALKLLKTEL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13C/15N/2H AGR2

#	Name	Isotope labeling	Concentration
1	AGR2	[U-13C; U-15N; U-2H]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13CH3 ILV labelled

#	Name	Isotope labeling	Concentration
6	AGR2	[U-13C; U-15N; U-2H]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	MES	natural abundance	20 mM
10	NaCl	natural abundance	100 mM

Sample #3

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

#	Name	Isotope labeling	Concentration
11	AGR2	[U-15N]	1 mM
12	Pf1 phage	natural abundance	10 mg
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %
15	MES	natural abundance	20 mM
16	NaCl	natural abundance	100 mM

Sample #4

Solvent system PEG, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
17	AGR2	[U-15N]	1 mM
18	PEG:Hexanol	natural abundance	5 %
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %
21	MES	natural abundance	20 mM
22	NaCl	natural abundance	100 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: 0.66 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: 0.66 ppm, Outliers: 1 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: 0.04 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LNS, Strand ID: A, B Detail

Release date

2013-01-06

Citation

Metastasis-promoting anterior gradient 2 protein has a dimeric thioredoxin fold structure and a role in cell adhesion
Patel, P., Clarke, C., Barraclough, D., Jowitt, T., Rudland, P., Barraclough, R., Lian, L.
J. Mol. Biol. (2013), 425, 929-943, PubMed 23274113 , DOI 10.1016/j.jmb.2012.12.009 , Abstract

Related entities 1. AGR2 residues 41-175, : 1 : 4 : 33 entities Detail

Interaction partners 1. AGR2 residues 41-175, : 17 interactors Detail

More details for 17 interactors identified by 9 citations

Experiments performed 13 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 298 K, pH 6.5, Details 13C/15N/2H AGR2

#	Name	Isotope labeling	Concentration
1	AGR2	[U-13C; U-15N; U-2H]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13CH3 ILV labelled

#	Name	Isotope labeling	Concentration
6	AGR2	[U-13C; U-15N; U-2H]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	MES	natural abundance	20 mM
10	NaCl	natural abundance	100 mM

3 3D HN(COCA)CB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13C/15N/2H AGR2

#	Name	Isotope labeling	Concentration
1	AGR2	[U-13C; U-15N; U-2H]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13C/15N/2H AGR2

#	Name	Isotope labeling	Concentration
1	AGR2	[U-13C; U-15N; U-2H]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13C/15N/2H AGR2

#	Name	Isotope labeling	Concentration
1	AGR2	[U-13C; U-15N; U-2H]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

6 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13C/15N/2H AGR2

#	Name	Isotope labeling	Concentration
1	AGR2	[U-13C; U-15N; U-2H]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

7 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13C/15N/2H AGR2

#	Name	Isotope labeling	Concentration
1	AGR2	[U-13C; U-15N; U-2H]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13CH3 ILV labelled

#	Name	Isotope labeling	Concentration
6	AGR2	[U-13C; U-15N; U-2H]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	MES	natural abundance	20 mM
10	NaCl	natural abundance	100 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13CH3 ILV labelled

#	Name	Isotope labeling	Concentration
6	AGR2	[U-13C; U-15N; U-2H]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	MES	natural abundance	20 mM
10	NaCl	natural abundance	100 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13CH3 ILV labelled

#	Name	Isotope labeling	Concentration
6	AGR2	[U-13C; U-15N; U-2H]	1 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %
9	MES	natural abundance	20 mM
10	NaCl	natural abundance	100 mM

11 IPAP

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
11	AGR2	[U-15N]	1 mM
12	Pf1 phage	natural abundance	10 mg
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %
15	MES	natural abundance	20 mM
16	NaCl	natural abundance	100 mM

12 IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system PEG, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
17	AGR2	[U-15N]	1 mM
18	PEG:Hexanol	natural abundance	5 %
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %
21	MES	natural abundance	20 mM
22	NaCl	natural abundance	100 mM

13 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 13C/15N/2H AGR2

#	Name	Isotope labeling	Concentration
1	AGR2	[U-13C; U-15N; U-2H]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	MES	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18178_2lns.nef
Input source #2: Coordindates	2lns.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

---40--------50--------60--------70--------80--------90-------100-------110-------120-------130-----
IDPFTPQTLSRGWGDQLIWTQTYEEALYKSKTSNKPLMIIHHLDECPHSQALKKVFAENKEIQKLAEQFVLLNLVYETTDKHLSPDGQYVPRIMFVDPSL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IDPFTPQTLSRGWGDQLIWTQTYEEALYKSKTSNKPLMIIHHLDECPHSQALKKVFAENKEIQKLAEQFVLLNLVYETTDKHLSPDGQYVPRIMFVDPSL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--140-------150-------160-------170-----
TVRADITGRYSNRLYAYEPADTALLLDNMKKALKLLKTEL
||||||||||||||||||||||||||||||||||||||||
TVRADITGRYSNRLYAYEPADTALLLDNMKKALKLLKTEL
-------110-------120-------130-------140

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

---40--------50--------60--------70--------80--------90-------100-------110-------120-------130-----
IDPFTPQTLSRGWGDQLIWTQTYEEALYKSKTSNKPLMIIHHLDECPHSQALKKVFAENKEIQKLAEQFVLLNLVYETTDKHLSPDGQYVPRIMFVDPSL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IDPFTPQTLSRGWGDQLIWTQTYEEALYKSKTSNKPLMIIHHLDECPHSQALKKVFAENKEIQKLAEQFVLLNLVYETTDKHLSPDGQYVPRIMFVDPSL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--140-------150-------160-------170-----
TVRADITGRYSNRLYAYEPADTALLLDNMKKALKLLKTEL
||||||||||||||||||||||||||||||||||||||||
TVRADITGRYSNRLYAYEPADTALLLDNMKKALKLLKTEL
-------110-------120-------130-------140

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	140	0	0	100.0
B	B	140	0	0	100.0

Content subtype: combined_18178_2lns.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	814		96.4 (chain: A, length: 140)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	558 (1)	noe	89.3 (chain: A, length: 140)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	95 (1)	undefined	15.0 (chain: A, length: 140)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	37 (1)	hbond	39.3 (chain: A, length: 140)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	179 (179)	.	86.4 (chain: A, length: 140)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	95 (95)	.	43.6 (chain: A, length: 140)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 96.4%
- Total number of assignments
  - ¹³C chemical shifts: 480
  - ¹H chemical shifts: 199
  - ¹⁵N chemical shifts: 135
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
51	GLN	CD	180.949
69	ASN	CG	177.979
85	GLN	CD	180.67
103	GLN	CD	180.109
147	ASN	CG	178.076
163	ASN	CG	175.776

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	670	474	70.7
¹H chemical shifts	888	199	22.4
¹⁵N chemical shifts	151	135	89.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	280	270	96.4
¹H chemical shifts	276	128	46.4
¹⁵N chemical shifts	132	128	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	390	204	52.3
¹H chemical shifts	612	71	11.6
¹⁵N chemical shifts	19	7	36.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	89	70	78.7
¹H chemical shifts	89	57	64.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	66	0	0.0
¹H chemical shifts	68	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 89.3%
- Total number of restraints: 558
- Weight of restraints: 1.0 (558)
- Potential type of restraints: square-well-parabolic (558)
- Range of distance target values: 2.01, 4.41 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 15.0%
  - Total number of restraints: 93
  - Weight of restraints: 1.0 (93)
  - Potential type of restraints: square-well-parabolic (93)
  - Range of distance target values: 4.0, 4.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 39.3%
    - Total number of restraints: 37
    - Weight of restraints: 1.0 (37)
    - Potential type of restraints: square-well-parabolic (37)
    - Range of distance target values: 2.0, 2.0 (Å)
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - 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: 140, Sequence coverage: 86.4%
- Total number of restraints: 179
- Total number of restraints per polymer type: 179
- Weight of restraints: 1.0 (179)
- Potential type of restraints: square-well-parabolic (179)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 140, Sequence coverage: 43.6%
- Total number of restraints: 95
- Potential type of restraints: undefined (95)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords adhesion, AGR2, Anterior-gradient Protein 2, cancer, metastasis, Thioredoxin-fold

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Found 1 Document (1.124 seconds)

BMRB: 18178

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. AGR2 residues 41-175, : 1 : 4 : 33 entities Detail

Interaction partners 1. AGR2 residues 41-175, : 17 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 7 contents Detail