BMRBj - BMREntryMaster

Found 1 Document (1.201 seconds)

BMRB: 4787

1HN6

Assignment of 1H, 13C and 15N resonances of domain III of the ectodomain of apical membrane antigen 1 from Plasmodium falciparum

Authors

Nair, M., Hodder, A.N., Hinds, M.G., Anders, R.F., Norton, R.S.

Assembly

Apical Membrane Antigen 1

Entity

1. Apical Membrane Antigen 1 (polymer, Thiol state: all disulfide bound), 122 monomers, 14329.91 Da Detail

MRGSHHHHHH GSEVENNFPC SLYKDEIMKE IERESKRIKL NDNDDEGNKK IIAPRIFISD DKDSLKCPCD PEMVSNSTCR FFVCKCVERR AEVTSNNEVV VKEEYKDEYA DIPEHKPTYD KM

Formula weight

14329.91 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	0:CYS20:SG	1:CYS79:SG

Source organism

Plasmodium falciparum

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 85.2 %, Completeness: 73.7 %, Completeness (bb): 80.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.7 % (1060 of 1439)	77.7 % (592 of 762)	67.1 % (371 of 553)	78.2 % (97 of 124)
Backbone	80.4 % (579 of 720)	81.3 % (196 of 241)	79.1 % (287 of 363)	82.8 % (96 of 116)
Sidechain	69.1 % (579 of 838)	76.0 % (396 of 521)	58.9 % (182 of 309)	12.5 % (1 of 8)
Aromatic	31.0 % (31 of 100)	62.0 % (31 of 50)	0.0 % (0 of 50)
Methyl	84.1 % (74 of 88)	97.7 % (43 of 44)	70.5 % (31 of 44)

1. Apical membrane antigen 1

MRGSHHHHHH GSEVENNFPC SLYKDEIMKE IERESKRIKL NDNDDEGNKK IIAPRIFISD DKDSLKCPCD PEMVSNSTCR FFVCKCVERR AEVTSNNEVV VKEEYKDEYA DIPEHKPTYD KM

Show sample condition

Sample #1

Temperature 303 (±0.2) K, pH 3.4 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

Temperature 303 (±0.2) K, pH 3.4 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	0.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	0.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	0.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	0.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.28 ppm, Outliers: 1 Detail

Release date

2001-02-13

Citation 1

Assignment of 1H, 13C and 15N resonances of domain III of the ectodomain of apical membrane antigen 1 from Plasmodium falciparum
Nair, M., Hodder, A.N., Hinds, M.G., Anders, R.F., Norton, R.S.
J. Biomol. NMR (2001), 19, 85-86, PubMed 11246861 , Abstract

Show more 2 citaions

Citation 2

The disulfide bond structure of Plasmodium apical membrane antigen-1
Hodder, A.N., Crewther, P.E., Matthew, M.L., Reid, G.E., Moritz, R.L., Simpson, R.J., Anders, R.F.
J. Biol. Chem. (1996), 271, 29446-29452, PubMed 8910611 , DOI 10.1074/jbc.271.46.29446 , Abstract

Citation 3

1H, 13C and 15N chemical shift referencing in biomolecular NMR
Wishart, D.S., Bigam, C.G., Yao, J., Abildgaard, F., Dyson, H.J., Oldfield, E., Markley, J.L., Sykes, B.D.
J. Biomol. NMR (1995), 6, 135-140, PubMed 8589602 , DOI 10.1007/bf00211777 , Abstract

Hide non-primary 2 citaions

Related entities 1. Apical Membrane Antigen 1, : 1 : 1 : 13 entities Detail

Experiments performed 9 experiments Detail

1 3D 1H-1H-15N NOESY

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker AMX (500 MHz)

Sample #1

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

2 3D 1H-1H-13C NOESY

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker AMX (500 MHz)

Sample #1

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

3 3D 1H-1H-15N TOCSY

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker AMX (500 MHz)

Sample #1

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

4 3D HNCA

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker AMX (500 MHz)

Sample #1

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

5 3D HNCO

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker AMX (500 MHz)

Sample #1

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

6 3D CBCA(CO)NH

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker AMX (500 MHz)

Sample #1

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

7 3D CCCONH

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker AMX (500 MHz)

Sample #1

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

8 3D 1H-13C-1H HCCH-TOCSY

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker AMX (500 MHz)

Sample #1

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

9 3D HNHA

Instrument

#1 Model Bruker DRX (600 MHz)

#2 Model Bruker AMX (500 MHz)

Sample #1

#	Name	Isotope labeling	Type	Concentration
1	Apical membrane antigen 1	[U-90% 15N]		0.5 ~ 1.0 mM

Sample #2

#	Name	Isotope labeling	Type	Concentration
2	Apical membrane antigen 1	[U-95% 13C[		0.5 ~ 1.0 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr4787_3.str
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)
1:20:CYS:SG	1:79:CYS:SG	oxidized, CA 56.8, CB 38.1 ppm	oxidized, CA 54.3, CB 39.0 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr4787_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	shift_set_1	Warning	1124		83.6 (chain: 1, length: 122)
1	Chemical shift references	chemical_shift_reference_one	OK	3		No information

Assigned chemical shifts

Saveframe: shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 122, Sequence coverage: 83.6%
- Total number of assignments
  - ¹⁵N chemical shifts: 96
  - ¹H chemical shifts: 670
  - ¹³C chemical shifts: 358
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
62	LYS	HZ1	7.42
62	LYS	HZ2	7.42
62	LYS	HZ3	7.42

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	131	96	73.3
¹H chemical shifts	762	583	76.5
¹³C chemical shifts	553	358	64.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	116	95	81.9
¹H chemical shifts	241	192	79.7
¹³C chemical shifts	244	187	76.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹⁵N chemical shifts	15	1	6.7
¹H chemical shifts	521	391	75.0
¹³C chemical shifts	309	171	55.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	42	87.5
¹³C chemical shifts	48	25	52.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	31	62.0
¹³C chemical shifts	50	0	0.0

Keywords NMR resonance assignments, antigen, malaria

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.201 seconds)

BMRB: 4787

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Apical Membrane Antigen 1, : 1 : 1 : 13 entities Detail

Experiments performed 9 experiments Detail

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Chemical shift validation 3 contents Detail