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Found 1 Document (0.831 seconds)

BMRB: 25560

2N1H

Solution structure of the GBII-beta MRH domain W409A point mutant

Authors

Olson, L.J., Peterson, F.C., Damhs, N.M.

Assembly

MRH-GIIb

Entity

1. MRH-GIIb (polymer, Thiol state: all disulfide bound), 94 monomers, 10417.75 Da Detail

YRAIKGMETK REIGGYTYKV VFYENVFQDS ILLGNFASQE GNVLKYENGQ SCANGPHRSA IVTVECGVEN EIVSVLEAQK CEYLIKMKSP AACS

Formula weight

10417.75 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS52:SG	1:CYS81:SG
2	disulfide	sing	1:CYS66:SG	1:CYS93:SG

Source organism

Schizosaccharomyces pombe

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.8 %, Completeness: 89.7 %, Completeness (bb): 92.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.7 % (970 of 1081)	92.2 % (517 of 561)	85.4 % (357 of 418)	94.1 % (96 of 102)
Backbone	92.3 % (517 of 560)	94.3 % (183 of 194)	90.5 % (248 of 274)	93.5 % (86 of 92)
Sidechain	88.0 % (534 of 607)	91.0 % (334 of 367)	82.6 % (190 of 230)	100.0 % (10 of 10)
Aromatic	68.3 % (56 of 82)	87.8 % (36 of 41)	48.8 % (20 of 41)
Methyl	93.0 % (93 of 100)	98.0 % (49 of 50)	88.0 % (44 of 50)

1. entity

YRAIKGMETK REIGGYTYKV VFYENVFQDS ILLGNFASQE GNVLKYENGQ SCANGPHRSA IVTVECGVEN EIVSVLEAQK CEYLIKMKSP AACS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1

#	Name	Isotope labeling	Concentration
1	MRH GIIb	[U-99% 13C; U-99% 15N]	0.7 mM
2	imidazole	[U-99% 2H]	10 mM
3	sodium chloride	natural abundance	150 mM
4	sodium azide	natural abundance	0.02 %
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

LACS Plot; CA

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

Referencing offset: -0.33 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.33 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.14 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.98 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N1H, Strand ID: A Detail

Release date

2015-12-06

Citation

Crystal structure and functional analyses of glucosdidase II's lectin domain: Insgihts into oligomannose recognition
Olson, L.J., Orsi, R., Peterson, F.C., Parodi, A.J., Kim, J.P., D'Alessio, C., Damhs, N.M.
Not known

Related entities 1. MRH-GIIb, : 1 : 4 : 11 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25560_2n1h.nef
Input source #2: Coordindates	2n1h.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:408:CYS:SG	A:437:CYS:SG	oxidized, CA 55.139, CB 44.133 ppm	oxidized, CA 57.722, CB 42.191 ppm	2.027
A:422:CYS:SG	A:449:CYS:SG	oxidized, CA 57.084, CB 39.228 ppm	oxidized, CA 55.786, CB 42.838 ppm	2.008

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

---360-----370-------380-------390-------400-------410-------420-------430-------440-------450
YRAIKGMETKREIGGYTYKVVFYENVFQDSILLGNFASQEGNVLKYENGQSCANGPHRSAIVTVECGVENEIVSVLEAQKCEYLIKMKSPAACS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
YRAIKGMETKREIGGYTYKVVFYENVFQDSILLGNFASQEGNVLKYENGQSCANGPHRSAIVTVECGVENEIVSVLEAQKCEYLIKMKSPAACS
--------10--------20--------30--------40--------50--------60--------70--------80--------90----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	94	0	0	100.0

Content subtype: combined_25560_2n1h.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	969		96.8 (chain: A, length: 94)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	1900 (1)	noe	94.7 (chain: A, length: 94)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	6 (1)	undefined	4.3 (chain: A, length: 94)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	99 (99)	.	79.8 (chain: A, length: 94)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 517
  - ¹³C chemical shifts: 356
  - ¹⁵N chemical shifts: 96
- 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	561	517	92.2
¹³C chemical shifts	418	356	85.2
¹⁵N chemical shifts	105	96	91.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	194	183	94.3
¹³C chemical shifts	188	166	88.3
¹⁵N chemical shifts	92	86	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	367	334	91.0
¹³C chemical shifts	230	190	82.6
¹⁵N chemical shifts	13	10	76.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	51	98.1
¹³C chemical shifts	52	46	88.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	36	87.8
¹³C chemical shifts	41	20	48.8

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 94.7%
- Total number of restraints: 1898
- Weight of restraints: 1.0 (1898)
- Potential type of restraints: upper-bound-parabolic (1898)
- Range of distance target values: 2.21, 5.5 (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: DYANA/DIANA_distance_constraints_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 4.3%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: upper-bound-parabolic (6)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 79.8%
- Total number of restraints: 99
- Total number of restraints per polymer type: 99
- Weight of restraints: 1.0 (99)
- Potential type of restraints: square-well-parabolic (99)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords hydrolase, NMR, lectin, MRH

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Found 1 Document (0.831 seconds)

BMRB: 25560

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MRH-GIIb, : 1 : 4 : 11 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail