BMRBj - BMREntryMaster

Found 1 Document (0.712 seconds)

BMRB: 18592

2LVX

MRH domain of the Glucosidase II beta subunit from S. pombe

Authors

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

Assembly

MRH domain

Entity

1. MRH domain (polymer, Thiol state: all disulfide bound), 94 monomers, 10532.88 Da Detail

YRAIKGMETK REIGGYTYKV VFYENVFQDS ILLGNFASQE GNVLKYENGQ SCWNGPHRSA IVTVECGVEN EIVSVLEAQK CEYLIKMKSP AACS

Formula weight

10532.88 Da

Entity Connection

disulfide 2 Detail

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

Source organism

Schizosaccharomyces pombe

Exptl. method

solution NMR

Refine. method

AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT.

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 90.6 %, Completeness (bb): 93.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.6 % (991 of 1094)	92.6 % (526 of 568)	86.8 % (367 of 423)	95.1 % (98 of 103)
Backbone	93.2 % (522 of 560)	94.8 % (184 of 194)	91.6 % (251 of 274)	94.6 % (87 of 92)
Sidechain	88.9 % (551 of 620)	91.4 % (342 of 374)	84.3 % (198 of 235)	100.0 % (11 of 11)
Aromatic	74.5 % (70 of 94)	91.5 % (43 of 47)	56.5 % (26 of 46)	100.0 % (1 of 1)
Methyl	92.9 % (91 of 98)	95.9 % (47 of 49)	89.8 % (44 of 49)

1. MRH domain

YRAIKGMETK REIGGYTYKV VFYENVFQDS ILLGNFASQE GNVLKYENGQ SCWNGPHRSA IVTVECGVEN EIVSVLEAQK CEYLIKMKSP AACS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.1, Details 1.0 mM MRH(357-450) U-15N/13C, 10 mM imidazole, 150 mM sodium chloride

#	Name	Isotope labeling	Concentration
1	imidazole	[U-100% 2H]	10 mM
2	sodium chloride	natural abundance	150 mM
3	H2O	natural abundance	95 %
4	D2O	[U-99% 2H]	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: -0.32 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: -0.32 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: -0.13 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: 0.94 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-04-28

Citation

Structure of the lectin mannose 6-phosphate receptor homology (MRH) domain of glucosidase II, an enzyme that regulates glycoprotein folding quality control in the endoplasmic reticulum
Olson, L.J., Orsi, R., Alculumbre, S.G., Peterson, F.C., Stigliano, I.D., Parodi, A.J., Dahms, C.
J. Biol. Chem. (2013), 288, 16460-16475, PubMed 23609449 , DOI 10.1074/jbc.M113.450239 , Abstract

Related entities 1. MRH domain, : 1 : 3 : 1 : 11 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18592_2lvx.nef
Input source #2: Coordindates	2lvx.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 58.109, CB 42.516 ppm	2.018
A:422:CYS:SG	A:449:CYS:SG	oxidized, CA 57.084, CB 39.228 ppm	oxidized, CA 55.786, CB 42.838 ppm	2.033

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
YRAIKGMETKREIGGYTYKVVFYENVFQDSILLGNFASQEGNVLKYENGQSCWNGPHRSAIVTVECGVENEIVSVLEAQKCEYLIKMKSPAACS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
YRAIKGMETKREIGGYTYKVVFYENVFQDSILLGNFASQEGNVLKYENGQSCWNGPHRSAIVTVECGVENEIVSVLEAQKCEYLIKMKSPAACS
--------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_18592_2lvx.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	980		96.8 (chain: A, length: 94)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2253 (1)	noe	95.7 (chain: A, length: 94)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	130 (130)	.	93.6 (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: 523
  - ¹³C chemical shifts: 361
  - 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	568	523	92.1
¹³C chemical shifts	423	361	85.3
¹⁵N chemical shifts	106	96	90.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	194	183	94.3
¹³C chemical shifts	188	167	88.8
¹⁵N chemical shifts	92	85	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	374	340	90.9
¹³C chemical shifts	235	194	82.6
¹⁵N chemical shifts	14	11	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	50	98.0
¹³C chemical shifts	51	45	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	41	87.2
¹³C chemical shifts	46	24	52.2
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 95.7%
- Total number of restraints: 2252
- Weight of restraints: 1.0 (2252)
- Potential type of restraints: upper-bound-parabolic (2252)
- Range of distance target values: 2.1, 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

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: 93.6%
- Total number of restraints: 130
- Total number of restraints per polymer type: 130
- Weight of restraints: 1.0 (130)
- Potential type of restraints: square-well-parabolic (130)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords glycobiology, Lectin, MRH domain, protein folding

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.712 seconds)

BMRB: 18592

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MRH domain, : 1 : 3 : 1 : 11 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail