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Found 1 Document (1.026 seconds)

BMRB: 18953

2M3C

Solution Structure of gammaM7-Crystallin

Authors

Mahler, B., Wu, Z.

Assembly

gammaM-crystallin

Entity

1. gammaM-crystallin (polymer, Thiol state: all free), 174 monomers, 20906.63 Da Detail

MGKIIFYEDR NFGGRYHECM SDCADLHSYF NRCHSIRVES GCFMVYDRTN FMGRQYFLRR GEYPDYMRTM GMNDCVRSCR MIPLHHGSFK MRLYEHSDMG GRMMELMDDC PNLMDRFNMS DFHSCHVMDG HWLVYEQPNY TGRQFYLRPG EYRSYNDWGG VTSRMGSIRR ITDL

Formula weight

20906.63 Da

Source organism

Danio rerio

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.3 %, Completeness: 76.2 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.2 % (1573 of 2065)	69.2 % (750 of 1084)	82.0 % (655 of 799)	92.3 % (168 of 182)
Backbone	96.2 % (995 of 1034)	96.4 % (346 of 359)	96.0 % (486 of 506)	96.4 % (163 of 169)
Sidechain	61.6 % (733 of 1189)	55.7 % (404 of 725)	71.8 % (324 of 451)	38.5 % (5 of 13)
Aromatic	15.5 % (41 of 264)	20.5 % (27 of 132)	9.2 % (12 of 130)	100.0 % (2 of 2)
Methyl	100.0 % (96 of 96)	100.0 % (48 of 48)	100.0 % (48 of 48)

1. entity

MGKIIFYEDR NFGGRYHECM SDCADLHSYF NRCHSIRVES GCFMVYDRTN FMGRQYFLRR GEYPDYMRTM GMNDCVRSCR MIPLHHGSFK MRLYEHSDMG GRMMELMDDC PNLMDRFNMS DFHSCHVMDG HWLVYEQPNY TGRQFYLRPG EYRSYNDWGG VTSRMGSIRR ITDL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 305 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	imidazole	[U-2H]	25 mM
2	potassium chloride	natural abundance	20 mM
3	DTT	natural abundance	2 mM
4	sodium azide	natural abundance	0.04 %
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

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: -0.48 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: -0.48 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: 0.02 ppm, Outliers: 1 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: -0.28 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2M3C, Strand ID: A Detail

Release date

2013-06-03

Citation

Structure and dynamics of the fish eye lens protein, γM7-crystallin
Mahler, B., Chen, Y., Ford, J., Thiel, C., Wistow, G., Wu, Z.
Biochemistry (2013), 52, 3579-3587, PubMed 23597261 , DOI 10.1021/bi400151c , Abstract

Related entities 1. gammaM-crystallin, : 1 : 1 : 267 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, RDC restraints	combined_18953_2m3c.nef
Input source #2: Coordindates	2m3c.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-------100
MGKIIFYEDRNFGGRYHECMSDCADLHSYFNRCHSIRVESGCFMVYDRTNFMGRQYFLRRGEYPDYMRTMGMNDCVRSCRMIPLHHGSFKMRLYEHSDMG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGKIIFYEDRNFGGRYHECMSDCADLHSYFNRCHSIRVESGCFMVYDRTNFMGRQYFLRRGEYPDYMRTMGMNDCVRSCRMIPLHHGSFKMRLYEHSDMG

-------110-------120-------130-------140-------150-------160-------170----
GRMMELMDDCPNLMDRFNMSDFHSCHVMDGHWLVYEQPNYTGRQFYLRPGEYRSYNDWGGVTSRMGSIRRITDL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GRMMELMDDCPNLMDRFNMSDFHSCHVMDGHWLVYEQPNYTGRQFYLRPGEYRSYNDWGGVTSRMGSIRRITDL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	174	0	0	100.0

Content subtype: combined_18953_2m3c.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1502		98.3 (chain: A, length: 174)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1143 (1)	noe	98.3 (chain: A, length: 174)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	41 (1)	noe	11.5 (chain: A, length: 174)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	131 (131)	.	75.3 (chain: A, length: 174)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 174, Sequence coverage: 98.3%
- Total number of assignments
  - ¹H chemical shifts: 689
  - ¹³C chemical shifts: 648
  - ¹⁵N chemical shifts: 165
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
111	PRO	N	176.27

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1084	689	63.6
¹³C chemical shifts	799	648	81.1
¹⁵N chemical shifts	202	164	81.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	359	347	96.7
¹³C chemical shifts	348	331	95.1
¹⁵N chemical shifts	169	162	95.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	725	342	47.2
¹³C chemical shifts	451	317	70.3
¹⁵N chemical shifts	33	2	6.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	64	98.5
¹³C chemical shifts	65	64	98.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	132	12	9.1
¹³C chemical shifts	130	5	3.8
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 174, Sequence coverage: 98.3%
- Total number of restraints: 1143
- Weight of restraints: 1.0 (1143)
- Potential type of restraints: square-well-parabolic (1143)
- Range of distance target values: 1.85, 4.15 (Å)
- Histogram of 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: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 174, Sequence coverage: 11.5%
  - Total number of restraints: 41
  - Weight of restraints: 1.0 (41)
  - Potential type of restraints: square-well-parabolic (41)
  - Range of distance target values: 2.9, 4.4 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 174, Sequence coverage: 75.3%
- Total number of restraints: 131
- Potential type of restraints: square-well-parabolic (131)
- Range of observed RDC values: -33.28, 20.76 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords beta/gamma crystallin, fish lens, methionine

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Found 1 Document (1.026 seconds)

BMRB: 18953

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. gammaM-crystallin, : 1 : 1 : 267 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail