BMRBj - BMREntryMaster

Found 1 Document (0.837 seconds)

BMRB: 19811

2MLB

NMR solution structure of a computational designed protein based on template of human erythrocytic ubiquitin

Authors

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

Assembly

a computational designed protein based on template of human erythrocytic ubiquitin

Entity

1. a computational designed protein based on template of human erythrocytic ubiquitin (polymer, Thiol state: not present), 79 monomers, 8549.746 Da Detail

MDTINITLPD GKTLTLTVTP EFTVKELAEE IARRLGLSPE DIKLTHNGKT LDPSLTLAEY GITPGSTITL EIKKKGGLE

Formula weight

8549.746 Da

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.4 %, Completeness (bb): 85.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.4 % (797 of 902)	95.5 % (445 of 466)	76.7 % (276 of 360)	100.0 % (76 of 76)
Backbone	85.6 % (397 of 464)	100.0 % (160 of 160)	70.9 % (163 of 230)	100.0 % (74 of 74)
Sidechain	92.5 % (472 of 510)	93.1 % (285 of 306)	91.6 % (185 of 202)	100.0 % (2 of 2)
Aromatic	27.3 % (6 of 22)	54.5 % (6 of 11)	0.0 % (0 of 11)
Methyl	97.4 % (113 of 116)	100.0 % (58 of 58)	94.8 % (55 of 58)

1. redesigned ubiquitin

MDTINITLPD GKTLTLTVTP EFTVKELAEE IARRLGLSPE DIKLTHNGKT LDPSLTLAEY GITPGSTITL EIKKKGGLE

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	redesigned ubiquitin	[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	D2O	[U-100% 2H]	10 %
6	H2O	natural abundance	90 %

Sample #2

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

#	Name	Isotope labeling	Concentration
7	redesigned ubiquitin	[U-100% 13C]	0.5 ~ 1.0 mM
8	phosphate buffer	natural abundance	25 mM
9	sodium chloride	natural abundance	100 mM
10	EDTA	natural abundance	2 mM
11	D2O	[U-100% 2H]	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-10-26

Citation

A comprehensive statistical energy function for protein design
Xiong, P., Wang, M., Zhou, X., Zhang, T., Zhang, J., Chen, Q., Liu, H.
Nat. Methods

Related entities 1. a computational designed protein based on template of human erythrocytic ubiquitin, : 1 : 719 entities Detail

Experiments performed 10 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	redesigned ubiquitin	[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	D2O	[U-100% 2H]	10 %
6	H2O	natural abundance	90 %

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	redesigned ubiquitin	[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	D2O	[U-100% 2H]	10 %
6	H2O	natural abundance	90 %

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	redesigned ubiquitin	[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	D2O	[U-100% 2H]	10 %
6	H2O	natural abundance	90 %

4 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	redesigned ubiquitin	[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	D2O	[U-100% 2H]	10 %
6	H2O	natural abundance	90 %

5 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	redesigned ubiquitin	[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	D2O	[U-100% 2H]	10 %
6	H2O	natural abundance	90 %

6 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	redesigned ubiquitin	[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	D2O	[U-100% 2H]	10 %
6	H2O	natural abundance	90 %

7 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
7	redesigned ubiquitin	[U-100% 13C]	0.5 ~ 1.0 mM
8	phosphate buffer	natural abundance	25 mM
9	sodium chloride	natural abundance	100 mM
10	EDTA	natural abundance	2 mM
11	D2O	[U-100% 2H]	100 %

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	redesigned ubiquitin	[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	D2O	[U-100% 2H]	10 %
6	H2O	natural abundance	90 %

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
7	redesigned ubiquitin	[U-100% 13C]	0.5 ~ 1.0 mM
8	phosphate buffer	natural abundance	25 mM
9	sodium chloride	natural abundance	100 mM
10	EDTA	natural abundance	2 mM
11	D2O	[U-100% 2H]	100 %

10 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
7	redesigned ubiquitin	[U-100% 13C]	0.5 ~ 1.0 mM
8	phosphate buffer	natural abundance	25 mM
9	sodium chloride	natural abundance	100 mM
10	EDTA	natural abundance	2 mM
11	D2O	[U-100% 2H]	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19811_2mlb.nef
Input source #2: Coordindates	2mlb.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---------
MDTINITLPDGKTLTLTVTPEFTVKELAEEIARRLGLSPEDIKLTHNGKTLDPSLTLAEYGITPGSTITLEIKKKGGLE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDTINITLPDGKTLTLTVTPEFTVKELAEEIARRLGLSPEDIKLTHNGKTLDPSLTLAEYGITPGSTITLEIKKKGGLE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0

Content subtype: combined_19811_2mlb.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	785		100.0 (chain: A, length: 79)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1669 (1)	noe	98.7 (chain: A, length: 79)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	34 (1)	hbond	32.9 (chain: A, length: 79)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	132 (132)	.	93.7 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 445
  - ¹³C chemical shifts: 264
  - ¹⁵N chemical shifts: 76
- 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	466	444	95.3
¹³C chemical shifts	360	264	73.3
¹⁵N chemical shifts	78	76	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	160	159	99.4
¹³C chemical shifts	158	79	50.0
¹⁵N chemical shifts	74	74	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	306	285	93.1
¹³C chemical shifts	202	185	91.6
¹⁵N chemical shifts	4	2	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	58	98.3
¹³C chemical shifts	59	55	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	6	54.5
¹³C chemical shifts	11	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 98.7%
- Total number of restraints: 1664
- Weight of restraints: 1.0 (1664)
- Potential type of restraints: square-well-parabolic (1664)
- Range of distance target values: 1.98, 4.56 (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: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 32.9%
  - Total number of restraints: 34
  - Weight of restraints: 1.0 (34)
  - Potential type of restraints: square-well-parabolic (34)
  - 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: 79, Sequence coverage: 93.7%
- Total number of restraints: 132
- Total number of restraints per polymer type: 132
- Weight of restraints: 1.0 (132)
- Potential type of restraints: square-well-parabolic (132)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NMR, protein design, Statistical energy Function, ubiquitin

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Found 1 Document (0.837 seconds)

BMRB: 19811

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. a computational designed protein based on template of human erythrocytic ubiquitin, : 1 : 719 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail