BMRBj - BMREntryMaster

Found 1 Document (0.523 seconds)

BMRB: 15380

5LDE

Crystal Polymorphism of GB1 Examined by Solid-State NMR Spectroscopy and X-ray Diffraction

Authors

Frericks-Schmidt, H.L., Sperling, L.J., Gao, Y., Wylie, B.J., Boettcher, J.M., Wilson, S.R., Rienstra, C.M.

Assembly

GB1

Entity

1. GB1 (polymer, Thiol state: not present), 56 monomers, 6222.757 Da Detail

MQYKLILNGK TLKGETTTEA VDAATAEKVF KQYANDNGVD GEWTYDDATK TFTVTE

Formula weight

6222.757 Da

Source organism

Streptococcus sp. 'group G'

Exptl. method

solid-state NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 100.0 %, Completeness: 92.9 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	92.9 % (288 of 310)	91.1 % (226 of 248)	100.0 % (62 of 62)
Backbone	100.0 % (220 of 220)	100.0 % (164 of 164)	100.0 % (56 of 56)
Sidechain	84.5 % (120 of 142)	83.8 % (114 of 136)	100.0 % (6 of 6)
Aromatic	21.4 % (6 of 28)	18.5 % (5 of 27)	100.0 % (1 of 1)
Methyl	100.0 % (32 of 32)	100.0 % (32 of 32)

1. GB1

MQYKLILNGK TLKGETTTEA VDAATAEKVF KQYANDNGVD GEWTYDDATK TFTVTE

Show sample condition

Sample

Solvent system microcrystals in excess motherliquor, Pressure 1 atm, Details Prepared using batch crystallization conditions with a protein solution of 10 mg/mL of GB1 in 50 mM sodium phosphate buffer (pH=5.5) and a reservoir solution of 55% MPD, 15% IPA and 50 mM NaCl in 7.5 mM sodium acetate buffer (pH=4.5)

#	Name	Isotope labeling	Type	Concentration
1	GB1	[U-100% 13C; U-100% 15N]		15 mg

Chem. Shift Complete2

Sequence coverage: 100.0 %, Completeness: 91.9 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	91.9 % (570 of 620)	90.1 % (447 of 496)	99.2 % (123 of 124)
Backbone	100.0 % (440 of 440)	100.0 % (328 of 328)	100.0 % (112 of 112)
Sidechain	82.4 % (234 of 284)	82.0 % (223 of 272)	91.7 % (11 of 12)
Aromatic	10.7 % (6 of 56)	9.3 % (5 of 54)	50.0 % (1 of 2)
Methyl	100.0 % (64 of 64)	100.0 % (64 of 64)

1. GB1

MQYKLILNGK TLKGETTTEA VDAATAEKVF KQYANDNGVD GEWTYDDATK TFTVTE

Show sample condition

Sample

Solvent system microcrystals in excess motherliquor, Pressure 1 atm, Details Prepared using batch crystallization conditions with a protein solution of 10 mg/mL of GB1 in 50 mM sodium phosphate buffer (pH=5.5) and a reservoir solution of 55% MPD, 25% IPA and 150 mM NaCl in 16.7 mM sodium acetate buffer (pH=4.5)

#	Name	Isotope labeling	Type	Concentration
2	GB1	[U-99% 13C; U-99% 15N]		17 mg

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	adamantane	alkane carbon	40.48 ppm	external	direct	1.0
¹⁵N	adamantane	alkane carbon	40.48 ppm	external	direct	1.0

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	adamantane	alkane carbon	40.48 ppm	external	direct	1.0
¹⁵N	adamantane	alkane carbon	40.48 ppm	external	direct	1.0

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	adamantane	alkane carbon	40.48 ppm	external	direct	1.0
¹⁵N	adamantane	alkane carbon	40.48 ppm	external	direct	1.0

Referencing offset: -0.25 ppm, Outliers: 2 Detail

Release date

2016-10-10

Citation

Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction
Frericks-Schmidt, H.L., Sperling, L.J., Gao, Y., Wylie, B.J., Boettcher, J.M., Wilson, S.R., Rienstra, C.M.
J. Phys. Chem. B (2007), 111, 14362-14369, PubMed 18052145 , DOI 10.1021/jp075531p , Abstract

Related entities 1. GB1, : 1 : 20 : 2 : 47 : 38 entities Detail

Interaction partners 1. GB1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 2D N(CA)CX

Instrument

Varian InfinityPlus - 500 MHz

Sample

State solid, Solvent system microcrystals in excess motherliquor, Pressure 1 atm, Details Prepared using batch crystallization conditions with a protein solution of 10 mg/mL of GB1 in 50 mM sodium phosphate buffer (pH=5.5) and a reservoir solution of 55% MPD, 15% IPA and 50 mM NaCl in 7.5 mM sodium acetate buffer (pH=4.5)

#	Name	Isotope labeling	Type	Concentration
1	GB1	[U-100% 13C; U-100% 15N]		15 mg

2 2D N(CO)CX

Instrument

Varian InfinityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	GB1	[U-100% 13C; U-100% 15N]		15 mg

3 3D NCACX

Instrument

Varian InfinityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	GB1	[U-100% 13C; U-100% 15N]		15 mg

4 3D NCOCX

Instrument

Varian InfinityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	GB1	[U-100% 13C; U-100% 15N]		15 mg

5 2D CC DARR mixing

Instrument

Varian InfinityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	GB1	[U-100% 13C; U-100% 15N]		15 mg

6 2D CC SPC5 mixing

Instrument

Varian InfinityPlus - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	GB1	[U-100% 13C; U-100% 15N]		15 mg

7 2D N(CA)CX

Instrument

Varian InfinityPlus - 500 MHz

Sample

State solid, Solvent system microcrystals in excess motherliquor, Pressure 1 atm, Details Prepared using batch crystallization conditions with a protein solution of 10 mg/mL of GB1 in 50 mM sodium phosphate buffer (pH=5.5) and a reservoir solution of 55% MPD, 25% IPA and 150 mM NaCl in 16.7 mM sodium acetate buffer (pH=4.5)

#	Name	Isotope labeling	Type	Concentration
2	GB1	[U-99% 13C; U-99% 15N]		17 mg

8 2D N(CO)CX

Instrument

Varian InfinityPlus - 500 MHz

Sample

State solid, Solvent system microcrystals in excess motherliquor, Pressure 1 atm, Details Prepared using batch crystallization conditions with a protein solution of 10 mg/mL of GB1 in 50 mM sodium phosphate buffer (pH=5.5) and a reservoir solution of 55% MPD, 25% IPA and 150 mM NaCl in 16.7 mM sodium acetate buffer (pH=4.5)

#	Name	Isotope labeling	Type	Concentration
2	GB1	[U-99% 13C; U-99% 15N]		17 mg

9 3D NCACX

Instrument

Varian InfinityPlus - 500 MHz

Sample

State solid, Solvent system microcrystals in excess motherliquor, Pressure 1 atm, Details Prepared using batch crystallization conditions with a protein solution of 10 mg/mL of GB1 in 50 mM sodium phosphate buffer (pH=5.5) and a reservoir solution of 55% MPD, 25% IPA and 150 mM NaCl in 16.7 mM sodium acetate buffer (pH=4.5)

#	Name	Isotope labeling	Type	Concentration
2	GB1	[U-99% 13C; U-99% 15N]		17 mg

10 3D NCOCX

Instrument

Varian InfinityPlus - 500 MHz

Sample

State solid, Solvent system microcrystals in excess motherliquor, Pressure 1 atm, Details Prepared using batch crystallization conditions with a protein solution of 10 mg/mL of GB1 in 50 mM sodium phosphate buffer (pH=5.5) and a reservoir solution of 55% MPD, 25% IPA and 150 mM NaCl in 16.7 mM sodium acetate buffer (pH=4.5)

#	Name	Isotope labeling	Type	Concentration
2	GB1	[U-99% 13C; U-99% 15N]		17 mg

11 2D CC DARR mixing

Instrument

Varian InfinityPlus - 500 MHz

Sample

State solid, Solvent system microcrystals in excess motherliquor, Pressure 1 atm, Details Prepared using batch crystallization conditions with a protein solution of 10 mg/mL of GB1 in 50 mM sodium phosphate buffer (pH=5.5) and a reservoir solution of 55% MPD, 25% IPA and 150 mM NaCl in 16.7 mM sodium acetate buffer (pH=4.5)

#	Name	Isotope labeling	Type	Concentration
2	GB1	[U-99% 13C; U-99% 15N]		17 mg

12 2D CC SPC5 mixing

Instrument

Varian InfinityPlus - 500 MHz

Sample

State solid, Solvent system microcrystals in excess motherliquor, Pressure 1 atm, Details Prepared using batch crystallization conditions with a protein solution of 10 mg/mL of GB1 in 50 mM sodium phosphate buffer (pH=5.5) and a reservoir solution of 55% MPD, 25% IPA and 150 mM NaCl in 16.7 mM sodium acetate buffer (pH=4.5)

#	Name	Isotope labeling	Type	Concentration
2	GB1	[U-99% 13C; U-99% 15N]		17 mg

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr15380_3.str
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

Content subtype: bmr15380_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	GB1_formulation_D_chemical_shifts	Warning	315	100.0 (chain: 1, length: 56)
2	Assigned chemical shifts	GB1_formulation_E_chemical_shifts	Warning	303	100.0 (chain: 1, length: 56)
1	Chemical shift references	chemical_shift_reference_1	Warning	2	No information

Assigned chemical shifts

Saveframe: GB1_formulation_D_chemical_shifts

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 56, Sequence coverage: 100.0%

--------10--------20--------30--------40--------50------
MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE

Total number of assignments
- ¹³C chemical shifts: 247
- ¹⁵N chemical shifts: 68

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	GLN	CD	180.29
3	TYR	CZ	158.03
4	LYS	NZ	33.19
8	ASN	CG	176.51
10	LYS	NZ	33.5
13	LYS	NZ	31.52
15	GLU	CD	181.96
19	GLU	CD	182.32
22	ASP	CG	179.77
27	GLU	CD	181.49
28	LYS	NZ	32.92
31	LYS	NZ	32.21
32	GLN	CD	179.86
33	TYR	CZ	159.52
35	ASN	CG	175.96
36	ASP	CG	177.66
37	ASN	CG	176.79
40	ASP	CG	180.79
42	GLU	CD	182.13
43	TRP	CD2	130.05
43	TRP	CE2	138.51
43	TRP	CG	111.74
45	TYR	CZ	157.49
46	ASP	CG	180.23
47	ASP	CG	179.6
50	LYS	NZ	33.95
56	GLU	CD	183.17

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	248	226	91.1
¹⁵N chemical shifts	62	62	100.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	112	112	100.0
¹⁵N chemical shifts	56	56	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	136	114	83.8
¹⁵N chemical shifts	6	6	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	33	33	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	27	5	18.5
¹⁵N chemical shifts	1	1	100.0

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

Saveframe: GB1_formulation_E_chemical_shifts

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 56, Sequence coverage: 100.0%

--------10--------20--------30--------40--------50------
MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE

Total number of assignments
- ¹³C chemical shifts: 236
- ¹⁵N chemical shifts: 67

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	GLN	CD	180.27
4	LYS	NZ	33.54
8	ASN	CG	176.48
10	LYS	NZ	33.9
13	LYS	NZ	31.98
15	GLU	CD	181.94
19	GLU	CD	182.44
22	ASP	CG	179.79
27	GLU	CD	181.52
28	LYS	NZ	33.37
31	LYS	NZ	32.33
32	GLN	CD	179.83
35	ASN	CG	176.05
36	ASP	CG	177.71
37	ASN	CG	176.8
40	ASP	CG	180.89
42	GLU	CD	181.95
46	ASP	CG	180.12
47	ASP	CG	176.63
50	LYS	NZ	34.36
56	GLU	CD	183.22

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	248	221	89.1
¹⁵N chemical shifts	62	61	98.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	112	112	100.0
¹⁵N chemical shifts	56	56	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	136	109	80.1
¹⁵N chemical shifts	6	5	83.3

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	33	33	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	27	0	0.0
¹⁵N chemical shifts	1	0	0.0

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

Keywords formulation chemistry, polymorphism, protein x-ray powder diffractio, single crystal diffraction, solid-state NMR, therapeutic proteins

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Found 1 Document (0.523 seconds)

BMRB: 15380

Sample

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. GB1, : 1 : 20 : 2 : 47 : 38 entities Detail

Interaction partners 1. GB1, : 1 interactors Detail

Experiments performed 12 experiments Detail

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Chemical shift validation 4 contents Detail