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Found 1 Document (1.504 seconds)

BMRB: 6785

Backbone resonance assignments for the Fv fragment of the catalytic antibody 6D9 complexed with a transition state analogue

Authors

Sakakura, M., Takahashi, H., Terasawa, H., Takeuchi, K., Fujii, I., Shimada, I.

Assembly

Fv frangment of 6D9

Entity

1. variable light chain (polymer, Thiol state: all disulfide bound), 115 monomers, 12533.06 Da Detail

MELVMTQTPL SLPVSLGDQA SISCRSSQTI VHSNGDTYLD WFLQKPGQSP KLLIYKVSNR FSGVPDRFSG SGSGTDFTLK ISRVEAEDLG VYYCFQGSHV PPTFGGGTKL EIKRA

2. variable heavy chain (polymer, Thiol state: all disulfide bound), 134 monomers, 14911.55 Da Detail

MQVQLLESGG GLVKPGGSLK LSCAASGFTF SNYAMSWVRQ TPEKRLEWVV SISSGGSIYY LDSVKGRFTV SRDNARNILY LQMTSLRSED TAMYFCARVS HYDGSRDWYF DVWGAGTSVT VSSAAALEHH HHHH

3. TSA (non-polymer), 228.199 Da

Total weight

27672.809 Da

Max. entity weight

14911.55 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS24:SG	1:CYS94:SG
2	disulfide	sing	2:CYS23:SG	2:CYS96:SG

Source organism

Mus musculus

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 53.4 %, Completeness: 26.9 %, Completeness (bb): 44.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	26.9 % (761 of 2826)	16.4 % (238 of 1453)	35.7 % (397 of 1113)	48.5 % (126 of 260)
Backbone	44.0 % (649 of 1476)	30.2 % (155 of 513)	51.3 % (371 of 723)	51.2 % (123 of 240)
Sidechain	14.4 % (227 of 1575)	8.8 % (83 of 940)	22.9 % (141 of 615)	15.0 % (3 of 20)
Aromatic	3.4 % (10 of 294)	3.4 % (5 of 147)	2.8 % (4 of 142)	20.0 % (1 of 5)
Methyl	11.9 % (30 of 252)	12.7 % (16 of 126)	11.1 % (14 of 126)

1. variable light chain

MELVMTQTPL SLPVSLGDQA SISCRSSQTI VHSNGDTYLD WFLQKPGQSP KLLIYKVSNR FSGVPDRFSG SGSGTDFTLK ISRVEAEDLG VYYCFQGSHV PPTFGGGTKL EIKRA

2. variable heavy chain

MQVQLLESGG GLVKPGGSLK LSCAASGFTF SNYAMSWVRQ TPEKRLEWVV SISSGGSIYY LDSVKGRFTV SRDNARNILY LQMTSLRSED TAMYFCARVS HYDGSRDWYF DVWGAGTSVT VSSAAALEHH HHHH

Show sample condition

Sample #1

Temperature 303 (±0.1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	variable light chain	[U-13C; U-15N]	protein	0.6 mM
2	variable heavy chain		protein	0.6 mM
3	TSA		ligand	2.7 mM
4	sodium phosphate		buffer	5 mM
5	sodium chloride		salt	200 mM

Sample #2

Temperature 303 (±0.1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
6	variable light chain	[U-80% 2H; U-13C; U-15N]	protein	0.5 mM
7	variable heavy chain	[U-80% 2H]	protein	0.5 mM
8	TSA		ligand	1 mM
9	sodium phosphate		buffer	5 mM
10	sodium chloride		salt	200 mM

Sample #3

Temperature 303 (±0.1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
16	variable light chain	[U-98% 2H; U-13C; U-15N]	protein	0.25 mM
17	variable heavy chain	[U-98% 2H; U-13C; U-15N]	protein	0.25 mM
18	TSA		ligand	0.3 mM
19	sodium phosphate		buffer	5 mM
20	sodium chloride		salt	50 mM

Chem. Shift Complete2

Sequence coverage: 55.0 %, Completeness: 26.1 %, Completeness (bb): 43.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	26.1 % (1476 of 5652)	16.4 % (478 of 2906)	33.8 % (753 of 2226)	47.1 % (245 of 520)
Backbone	43.2 % (1276 of 2952)	30.7 % (315 of 1026)	49.7 % (719 of 1446)	50.4 % (242 of 480)
Sidechain	13.4 % (423 of 3150)	8.6 % (162 of 1880)	21.0 % (258 of 1230)	7.5 % (3 of 40)
Aromatic	1.9 % (11 of 588)	2.0 % (6 of 294)	1.4 % (4 of 284)	10.0 % (1 of 10)
Methyl	12.9 % (65 of 504)	14.3 % (36 of 252)	11.5 % (29 of 252)

1. variable light chain

MELVMTQTPL SLPVSLGDQA SISCRSSQTI VHSNGDTYLD WFLQKPGQSP KLLIYKVSNR FSGVPDRFSG SGSGTDFTLK ISRVEAEDLG VYYCFQGSHV PPTFGGGTKL EIKRA

2. variable heavy chain

MQVQLLESGG GLVKPGGSLK LSCAASGFTF SNYAMSWVRQ TPEKRLEWVV SISSGGSIYY LDSVKGRFTV SRDNARNILY LQMTSLRSED TAMYFCARVS HYDGSRDWYF DVWGAGTSVT VSSAAALEHH HHHH

Show sample condition

Sample #1

Temperature 303 (±0.1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
11	variable light chain	[U-80% 2H]	protein	0.6 mM
12	variable heavy chain	[U-80% 2H; U-13C; U-15N]	protein	0.6 mM
13	TSA		ligand	0.8 mM
14	sodium phosphate		buffer	5 mM
15	sodium chloride		salt	200 mM

Sample #2

Temperature 303 (±0.1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
16	variable light chain	[U-98% 2H; U-13C; U-15N]	protein	0.25 mM
17	variable heavy chain	[U-98% 2H; U-13C; U-15N]	protein	0.25 mM
18	TSA		ligand	0.3 mM
19	sodium phosphate		buffer	5 mM
20	sodium chloride		salt	50 mM

LACS Plot; CA

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

Referencing offset: 0.36 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.36 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.66 ppm, Outliers: 5 Detail

Release date

2005-12-19

Citation 1

Backbone resonance assignments for the Fv fragment of catalytic antibody 6D9 complexed with a transition state analogue
Sakakura, M., Takahashi, H., Terasawa, H., Takeuchi, K., Fujii, I., Shimada, I.
J. Biomol. NMR (2005), 33, 282-282, PubMed 16341758 , DOI 10.1007/s10858-005-3870-x , Abstract

Show more 2 citaions

Citation 2

A structural basis for transition-state stabilization in antibody-catalyzed hydrolysis: crystal structures of an abzyme at 1. 8 A resolution
Kristensen, O., Vassylyev, D.G., Tanaka, F., Morikawa, K., Fujii, I.
J. Mol. Biol. (1998), 281, 501-511, PubMed 9698565 , DOI 10.1006/jmbi.1998.1940 , Abstract

Citation 3

Practical introduction to theory and implementation of multinuclear, multidimensional nuclear magnetic resonance experiments
Edison, A.S., Abildgaard, F., Westler, W.M., Mooberry, E.S., Markley, J.L.
Methods. Enzymol. (1994), 239, 3-79, PubMed 7830587 , DOI: , Abstract

Hide non-primary 2 citaions

Entries sharing articles BMRB: 1 entries Detail

BMRB: 4001 released on 1996-01-28
Title 1H, 13C, and 15N resonance assignments for reduced apo-S100beta

Related entities 1. variable light chain, : 253 entities Detail

Related entities 2. variable heavy chain, : 215 entities Detail

Sample

State isotropic, Temperature 303 (±0.1) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Type	Concentration
16	variable light chain	[U-98% 2H; U-13C; U-15N]	protein	0.25 mM
17	variable heavy chain	[U-98% 2H; U-13C; U-15N]	protein	0.25 mM
18	TSA		ligand	0.3 mM
19	sodium phosphate		buffer	5 mM
20	sodium chloride		salt	50 mM

Chemical shift validation 6 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr6785_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	OK

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:24:CYS:SG	1:94:CYS:SG	oxidized, CA 55.416, CB 47.964 ppm	oxidized, CA 53.417, CB 44.658 ppm	n/a
2:23:CYS:SG	2:96:CYS:SG	unknown	unknown	n/a

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

None

Non-standard residues

None

Content subtype: bmr6785_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	OK	528	98.3 (chain: 1, length: 115)
2	Assigned chemical shifts	chem_shift_list_2	OK	541	90.3 (chain: 2, length: 134)
1	Chemical shift references	chemical_shift_referencing	OK	3	No information

Assigned chemical shifts

Saveframe: chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 115, Sequence coverage: 98.3%
- Total number of assignments
  - ¹³C chemical shifts: 317
  - ¹H chemical shifts: 106
  - ¹⁵N chemical shifts: 105
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1
Saveframe: chem_shift_list_2
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 134, Sequence coverage: 90.3%
- Total number of assignments
  - ¹³C chemical shifts: 322
  - ¹H chemical shifts: 110
  - ¹⁵N chemical shifts: 109
- Completeness of assignments
  - Entity_assemble_ID: 2
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	516	317	61.4
¹H chemical shifts	681	106	15.6
¹⁵N chemical shifts	122	105	86.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	230	219	95.2
¹H chemical shifts	235	105	44.7
¹⁵N chemical shifts	108	104	96.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	286	98	34.3
¹H chemical shifts	446	1	0.2
¹⁵N chemical shifts	14	1	7.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	61	2	3.3
¹H chemical shifts	61	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	55	0	0.0
¹H chemical shifts	56	1	1.8
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	597	322	53.9
¹H chemical shifts	772	110	14.2
¹⁵N chemical shifts	151	109	72.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	268	224	83.6
¹H chemical shifts	278	110	39.6
¹⁵N chemical shifts	132	109	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	329	98	29.8
¹H chemical shifts	494	0	0.0
¹⁵N chemical shifts	19	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	71	9	12.7
¹H chemical shifts	71	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	87	0	0.0
¹H chemical shifts	91	0	0.0
¹⁵N chemical shifts	4	0	0.0

Keywords catalytic antibody, Fv fragment, heteronuclear NMR, resonance assignments, Fab, transition-state stabilization, X-ray crystallography

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Found 1 Document (1.504 seconds)

BMRB: 6785

Sample #1

Sample #2

Sample #3

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. variable light chain, : 253 entities Detail

Related entities 2. variable heavy chain, : 215 entities Detail

Interaction partners 1. variable light chain, : 4 interactors Detail

Experiments performed 8 experiments Detail

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Chemical shift validation 6 contents Detail