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Found 1 Document (0.534 seconds)

BMRB: 19085

2M5X

Novel method of protein purification for structural research. Example of ultra high resolution structure of SPI-2 inhibitor by X-ray and NMR spectroscopy.

Authors

Lenarcic Zivkovic, M., Dvornyk, A., Kludkiewicz, B., Kopera, E., Zagorski-Ostoja, W., Grzelak, K., Zhukov, I., Bal, W.

Assembly

SPI-2 inhibitor

Entity

1. SPI-2 inhibitor (polymer, Thiol state: all disulfide bound), 40 monomers, 4314.717 Da Detail

EAAVCTTEWD PVCGKDGKTY SNLCWLNEAG VGLDHEGECL

Formula weight

4314.717 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS5:SG	1:CYS24:SG
2	disulfide	sing	1:CYS13:SG	1:CYS39:SG

Source organism

Galleria mellonella

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 83.2 %, Completeness (bb): 76.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.2 % (351 of 422)	95.8 % (205 of 214)	63.0 % (104 of 165)	97.7 % (42 of 43)
Backbone	76.5 % (182 of 238)	97.6 % (82 of 84)	53.9 % (62 of 115)	97.4 % (38 of 39)
Sidechain	91.3 % (200 of 219)	94.6 % (123 of 130)	85.9 % (73 of 85)	100.0 % (4 of 4)
Aromatic	83.3 % (30 of 36)	88.9 % (16 of 18)	75.0 % (12 of 16)	100.0 % (2 of 2)
Methyl	90.0 % (36 of 40)	90.0 % (18 of 20)	90.0 % (18 of 20)

1. GmSPI 2

EAAVCTTEWD PVCGKDGKTY SNLCWLNEAG VGLDHEGECL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	GmSPI 2	natural abundance		0.5 mM

Protein Blocks Logo

Calculated from 17 models in PDB: 2M5X, Strand ID: A Detail

Release date

2014-03-09

Citation

Ultrahigh resolution protein structure enabled by a non-enzymatic tag removal method. X-ray and NMR study of SPI-2 inhibitor
Kopera, E., Krzywda, S., Lenarcic Zivkovic, M., Dvornyk, A., Kludkiewicz, B., Grzelak, K., Zhukov, I., Zagorski-Ostoja, W., Jaskolski, M., Bal, W.
Not known

Related entities 1. SPI-2 inhibitor, : 1 : 1 : 212 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19085_2m5x.nef
Input source #2: Coordindates	2m5x.cif
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)
A:5:CYS:SG	A:24:CYS:SG	oxidized, CB 35.325 ppm	oxidized, CA 60.622, CB 35.293 ppm	2.027
A:13:CYS:SG	A:39:CYS:SG	oxidized, CA 53.837, CB 38.384 ppm	oxidized, CB 37.325 ppm	2.022

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
EAAVCTTEWDPVCGKDGKTYSNLCWLNEAGVGLDHEGECL
||||||||||||||||||||||||||||||||||||||||
EAAVCTTEWDPVCGKDGKTYSNLCWLNEAGVGLDHEGECL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	40	0	0	100.0

Content subtype: combined_19085_2m5x.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	343		100.0 (chain: A, length: 40)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	556 (1)	noe	95.0 (chain: A, length: 40)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	4 (1)	undefined	10.0 (chain: A, length: 40)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 205
  - ¹³C chemical shifts: 96
  - ¹⁵N chemical shifts: 42
- 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	214	205	95.8
¹³C chemical shifts	165	96	58.2
¹⁵N chemical shifts	43	42	97.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	82	97.6
¹³C chemical shifts	80	25	31.2
¹⁵N chemical shifts	39	38	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	130	123	94.6
¹³C chemical shifts	85	71	83.5
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	18	90.0
¹³C chemical shifts	20	18	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	16	88.9
¹³C chemical shifts	16	12	75.0
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 95.0%
- Total number of restraints: 552
- Weight of restraints: 1.0 (552)
- Potential type of restraints: square-well-parabolic (552)
- Range of distance target values: 1.31, 2.75 (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: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 40, Sequence coverage: 10.0%
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: square-well-parabolic (4)
  - Range of distance target values: 1.01, 1.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords Kazal family, serine protease inhibitor, SPI-2

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Found 1 Document (0.534 seconds)

BMRB: 19085

Sample

Related entities 1. SPI-2 inhibitor, : 1 : 1 : 212 entities Detail

Experiments performed 5 experiments Detail

Instrument

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NMR combined restraints 4 contents Detail