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BMRB: 19879

2MN4

NMR solution structure of a computational designed protein based on structure template 1cy5

Authors

Xiong, P., Wang, M., Zhang, J., Chen, Q., Liu, H.

Assembly

a computational designed protein based on structure template 1cy5

Entity

1. a computational designed protein based on structure template 1cy5 (polymer, Thiol state: not present), 94 monomers, 10732.40 Da Detail

MTPEQREFLP EILAEIIANL DPTKILEELL RRGLLTPAEL QEVLDLKTPE EQAKKLIDFI LKLSPADVQA RINVLRAHGY QALADKLNKY LTLE

Formula weight

10732.4 Da

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 74.5 %, Completeness: 61.7 %, Completeness (bb): 61.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	61.7 % (708 of 1148)	65.1 % (392 of 602)	55.1 % (248 of 450)	70.8 % (68 of 96)
Backbone	61.2 % (338 of 552)	69.6 % (128 of 184)	52.1 % (146 of 280)	72.7 % (64 of 88)
Sidechain	63.7 % (438 of 688)	63.2 % (264 of 418)	64.9 % (170 of 262)	50.0 % (4 of 8)
Aromatic	15.0 % (6 of 40)	30.0 % (6 of 20)	0.0 % (0 of 20)
Methyl	72.2 % (104 of 144)	72.2 % (52 of 72)	72.2 % (52 of 72)

1. entity

MTPEQREFLP EILAEIIANL DPTKILEELL RRGLLTPAEL QEVLDLKTPE EQAKKLIDFI LKLSPADVQA RINVLRAHGY QALADKLNKY LTLE

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	phosphate buffer	natural abundance	25 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	2 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
6	phosphate buffer	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	EDTA	natural abundance	2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2MN4, Strand ID: A Detail

Release date

2014-10-26

Citation

Boost computational protein design with a comprehensive statistical energy function and an in vivo experimental approach
Xiong, P., Wang, M., Zhou, X., Zhang, T., Zhang, J., Chen, Q., Liu, H.
Nat. Struct. Biol.

Related entities 1. a computational designed protein based on structure template 1cy5, : 1 : 14 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	phosphate buffer	natural abundance	25 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	2 mM

2 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	phosphate buffer	natural abundance	25 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	2 mM

3 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	phosphate buffer	natural abundance	25 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	2 mM

4 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	phosphate buffer	natural abundance	25 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	2 mM

5 3D H(CCO)NH

Instrument

Bruker DMX - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	phosphate buffer	natural abundance	25 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	2 mM

6 3D HCCH-TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
6	phosphate buffer	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	EDTA	natural abundance	2 mM

7 3D HCCH-COSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
6	phosphate buffer	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	EDTA	natural abundance	2 mM

8 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	phosphate buffer	natural abundance	25 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	2 mM

9 3D 1H-13C NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
6	phosphate buffer	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	EDTA	natural abundance	2 mM

10 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

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

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
2	phosphate buffer	natural abundance	25 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	2 mM

11 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	protein	[U-100% 13C; U-100% 15N]	0.5 ~ 1.0 mM
6	phosphate buffer	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	EDTA	natural abundance	2 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19879_2mn4.nef
Input source #2: Coordindates	2mn4.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

--------------10--------20--------30--------40--------50--------60--------70--------80--------90----
HHHHHHMTPEQREFLPEILAEIIANLDPTKILEELLRRGLLTPAELQEVLDLKTPEEQAKKLIDFILKLSPADVQARINVLRAHGYQALADKLNKYLTLE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HHHHHHMTPEQREFLPEILAEIIANLDPTKILEELLRRGLLTPAELQEVLDLKTPEEQAKKLIDFILKLSPADVQARINVLRAHGYQALADKLNKYLTLE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---100
HHHHHH
||||||
HHHHHH
------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	106	0	0	100.0

Content subtype: combined_19879_2mn4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	621		57.5 (chain: A, length: 106)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1632 (1)	noe	88.7 (chain: A, length: 106)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	38 (1)	hbond	29.2 (chain: A, length: 106)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	164 (164)	.	87.7 (chain: A, length: 106)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 57.5%
- Total number of assignments
  - ¹H chemical shifts: 350
  - ¹³C chemical shifts: 214
  - ¹⁵N chemical shifts: 57
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	674	350	51.9
¹³C chemical shifts	510	214	42.0
¹⁵N chemical shifts	113	57	50.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	116	55.8
¹³C chemical shifts	212	61	28.8
¹⁵N chemical shifts	100	54	54.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	466	234	50.2
¹³C chemical shifts	298	153	51.3
¹⁵N chemical shifts	13	3	23.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	46	63.0
¹³C chemical shifts	73	47	64.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	6	13.6
¹³C chemical shifts	44	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 88.7%
- Total number of restraints: 1629
- Weight of restraints: 1.0 (1629)
- Potential type of restraints: square-well-parabolic (1629)
- Range of distance target values: 2.35, 4.5 (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: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 29.2%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 87.7%
- Total number of restraints: 164
- Total number of restraints per polymer type: 164
- Weight of restraints: 1.0 (164)
- Potential type of restraints: square-well-parabolic (164)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords alpha-helical Greek, protein design, protein evolution, Statistical energy Function

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Found 1 Document (0.642 seconds)

BMRB: 19879

Sample #1

Sample #2

Related entities 1. a computational designed protein based on structure template 1cy5, : 1 : 14 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail