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Found 1 Document (0.839 seconds)

BMRB: 18415

2LS8

Solution structure of human C-type lectin domain family 4 member D

Authors

Harris, R., Gaudette, J., Bandaranayake, A.D., Banu, R., Bonanno, J.B., Calarese, D.A., Celikgil, A., Chamala, S., Chan, M.K., Chaparro, R., Evans, B., Garforth, S., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Lim, S., Love, J., Matikainen, B., Patel, H., Seidel, R.D., Smith, B., Stead, M., Girvin, M.E., Almo, S.C.

Assembly

human C-type lectin domain family 4 member D

Entity

1. human C-type lectin domain family 4 member D (polymer, Thiol state: all disulfide bound), 156 monomers, 18586.51 Da Detail

MVCPIDWRAF QSNCYFPLTD NKTWAESERN CSGMGAHLMT ISTEAEQNFI IQFLDRRLSY FLGLRDENAK GQWRWVDQTP FNPRRVFWHK NEPDNSQGEN CVVLVYNQDK WAWNDVPCNF EASRICKIPG TTLNAENLYF QSHHHHHHWS HPQFEK

Formula weight

18586.51 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS14:SG
2	disulfide	sing	1:CYS31:SG	1:CYS126:SG
3	disulfide	sing	1:CYS101:SG	1:CYS118:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 92.3 %, Completeness (bb): 92.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.3 % (1754 of 1900)	92.1 % (914 of 992)	92.6 % (675 of 729)	92.2 % (165 of 179)
Backbone	92.0 % (846 of 920)	91.6 % (284 of 310)	92.6 % (428 of 462)	90.5 % (134 of 148)
Sidechain	92.8 % (1049 of 1130)	92.4 % (630 of 682)	93.0 % (388 of 417)	100.0 % (31 of 31)
Aromatic	88.3 % (233 of 264)	88.6 % (117 of 132)	87.1 % (108 of 124)	100.0 % (8 of 8)
Methyl	96.6 % (114 of 118)	93.2 % (55 of 59)	100.0 % (59 of 59)

1. C-type lectin

MVCPIDWRAF QSNCYFPLTD NKTWAESERN CSGMGAHLMT ISTEAEQNFI IQFLDRRLSY FLGLRDENAK GQWRWVDQTP FNPRRVFWHK NEPDNSQGEN CVVLVYNQDK WAWNDVPCNF EASRICKIPG TTLNAENLYF QSHHHHHHWS HPQFEK

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	C-type lectin	[U-13C; U-15N]	1 mM
2	sodium acetate	natural abundance	10 mM
3	EDTA	natural abundance	0.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	C-type lectin	[U-13C; U-15N]	1 mM
7	sodium acetate	natural abundance	10 mM
8	EDTA	natural abundance	0.1 mM
9	D2O	natural abundance	100 %

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: -0.05 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: -0.05 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: 0.06 ppm, Outliers: 6 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: 0.14 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LS8, Strand ID: A Detail

Release date

2012-05-21

Related entities 1. human C-type lectin domain family 4 member D, : 1 : 3 : 241 entities Detail

Interaction partners 1. human C-type lectin domain family 4 member D, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	C-type lectin	[U-13C; U-15N]	1 mM
2	sodium acetate	natural abundance	10 mM
3	EDTA	natural abundance	0.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 15N NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	C-type lectin	[U-13C; U-15N]	1 mM
2	sodium acetate	natural abundance	10 mM
3	EDTA	natural abundance	0.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 13C CT-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	C-type lectin	[U-13C; U-15N]	1 mM
7	sodium acetate	natural abundance	10 mM
8	EDTA	natural abundance	0.1 mM
9	D2O	natural abundance	100 %

4 aromatic 13C CT-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	C-type lectin	[U-13C; U-15N]	1 mM
7	sodium acetate	natural abundance	10 mM
8	EDTA	natural abundance	0.1 mM
9	D2O	natural abundance	100 %

5 13C NOESY-HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	C-type lectin	[U-13C; U-15N]	1 mM
7	sodium acetate	natural abundance	10 mM
8	EDTA	natural abundance	0.1 mM
9	D2O	natural abundance	100 %

6 13C aromatic NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
6	C-type lectin	[U-13C; U-15N]	1 mM
7	sodium acetate	natural abundance	10 mM
8	EDTA	natural abundance	0.1 mM
9	D2O	natural abundance	100 %

7 HNCO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	C-type lectin	[U-13C; U-15N]	1 mM
2	sodium acetate	natural abundance	10 mM
3	EDTA	natural abundance	0.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

8 HNCACO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	C-type lectin	[U-13C; U-15N]	1 mM
2	sodium acetate	natural abundance	10 mM
3	EDTA	natural abundance	0.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

9 HNCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	C-type lectin	[U-13C; U-15N]	1 mM
2	sodium acetate	natural abundance	10 mM
3	EDTA	natural abundance	0.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

10 HNCOCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	C-type lectin	[U-13C; U-15N]	1 mM
2	sodium acetate	natural abundance	10 mM
3	EDTA	natural abundance	0.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

11 HNCACB

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	C-type lectin	[U-13C; U-15N]	1 mM
2	sodium acetate	natural abundance	10 mM
3	EDTA	natural abundance	0.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

12 CBCACONH

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 4.5, Details 10mM Na acetate buffer, pH 4.5, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
1	C-type lectin	[U-13C; U-15N]	1 mM
2	sodium acetate	natural abundance	10 mM
3	EDTA	natural abundance	0.1 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18415_2ls8.nef
Input source #2: Coordindates	2ls8.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:3:CYS:SG	A:14:CYS:SG	oxidized, CA 52.044, CB 39.461 ppm	oxidized, CA 53.685, CB 44.019 ppm	2.018
A:31:CYS:SG	A:126:CYS:SG	oxidized, CA 56.41, CB 34.709 ppm	oxidized, CA 51.84, CB 39.141 ppm	2.021
A:101:CYS:SG	A:118:CYS:SG	oxidized, CA 59.338, CB 43.778 ppm	oxidized, CA 58.904, CB 43.841 ppm	2.016

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
MVCPIDWRAFQSNCYFPLTDNKTWAESERNCSGMGAHLMTISTEAEQNFIIQFLDRRLSYFLGLRDENAKGQWRWVDQTPFNPRRVFWHKNEPDNSQGEN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVCPIDWRAFQSNCYFPLTDNKTWAESERNCSGMGAHLMTISTEAEQNFIIQFLDRRLSYFLGLRDENAKGQWRWVDQTPFNPRRVFWHKNEPDNSQGEN

-------110-------120-------130-------140-------150------
CVVLVYNQDKWAWNDVPCNFEASRICKIPGTTLNAENLYFQSHHHHHHWSHPQFEK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CVVLVYNQDKWAWNDVPCNFEASRICKIPGTTLNAENLYFQSHHHHHHWSHPQFEK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	156	0	0	100.0

Content subtype: combined_18415_2ls8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1765		96.8 (chain: A, length: 156)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2780 (1)	noe	89.7 (chain: A, length: 156)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	148 (1)	noe	53.8 (chain: A, length: 156)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	9 (1)	disulfide_bond	3.8 (chain: A, length: 156)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	72 (1)	hbond	32.1 (chain: A, length: 156)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	167 (167)	.	72.4 (chain: A, length: 156)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 923
  - ¹³C chemical shifts: 673
  - ¹⁵N chemical shifts: 169
- 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)
60	TYR	HH	9.696

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	992	922	92.9
¹³C chemical shifts	729	673	92.3
¹⁵N chemical shifts	188	169	89.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	310	285	91.9
¹³C chemical shifts	312	289	92.6
¹⁵N chemical shifts	148	131	88.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	682	637	93.4
¹³C chemical shifts	417	384	92.1
¹⁵N chemical shifts	40	38	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	62	100.0
¹³C chemical shifts	62	62	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	132	117	88.6
¹³C chemical shifts	124	108	87.1
¹⁵N chemical shifts	8	8	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 89.7%
- Total number of restraints: 2763
- Weight of restraints: 1.0 (2763)
- Potential type of restraints: square-well-parabolic (2763)
- Range of distance target values: 2.05, 4.9 (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: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 53.8%
  - Total number of restraints: 147
  - Weight of restraints: 1.0 (147)
  - Potential type of restraints: square-well-parabolic (147)
  - Range of distance target values: 2.4, 4.3 (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_6
    - Status: OK
    - Experiment type: disulfide_bond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 3.8%
    - Total number of restraints: 9
    - Weight of restraints: 1.0 (9)
    - Potential type of restraints: square-well-parabolic (9)
    - Range of distance target values: 2.02, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_5
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 32.1%
      - Total number of restraints: 72
        Total hydrogen bond restraints: 72
        O...h-N: 14
        O...H-x: 14
        Long range: 44
        O...h-N: 22
        O...H-x: 22
      - Weight of restraints: 1.0 (72)
        Total hydrogen bond restraints: 1.0 (72)
        O...h-N: 1.0 (14)
        O...H-x: 1.0 (14)
        Long range: 1.0 (44)
        O...h-N: 1.0 (22)
        O...H-x: 1.0 (22)
      - Potential type of restraints: square-well-parabolic (72)
        Total hydrogen bond restraints: square-well-parabolic (72)
        O...h-N: square-well-parabolic (14)
        O...H-x: square-well-parabolic (14)
        Long range: square-well-parabolic (44)
        O...h-N: square-well-parabolic (22)
        O...H-x: square-well-parabolic (22)
      - Range of distance target values: 1.7, 2.7 (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: 156, Sequence coverage: 72.4%
- Total number of restraints: 167
- Total number of restraints per polymer type: 167
- Weight of restraints: 1.0 (167)
- Potential type of restraints: square-well-parabolic (167)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords C-type lectin, New York Structural Genomics Research Consortium, STRUCTURAL GENOMICS

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Found 1 Document (0.839 seconds)

BMRB: 18415

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. human C-type lectin domain family 4 member D, : 1 : 3 : 241 entities Detail

Interaction partners 1. human C-type lectin domain family 4 member D, : 1 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 7 contents Detail