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Biological Magnetic Resonance Data Bank


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BMRB Entry 18415

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18415
MolProbity Validation Chart

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

Deposition date: 2012-04-23 Original release date: 2012-05-22

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

Citation: Harris, R.; Gaudette, J.; Bandaranayake, A.; Banu, R.; Bonanno, J.; Calarese, D.; Celikgil, A.; Chamala, S.; Chan, M.; Chaparro, R.; Evans, B.; Garforth, S.; Gizzi, A.; Hillerich, B.; Kar, A.; Lafleur, J.; Lim, S.; Love, J.; Matikainen, B.; Patel, H.; Seidel, R.; Smith, B.; Stead, M.; Girvin, M.; Almo, S.. "Solution structure of human C-type lectin domain family 4 member D"  To be published ., .-..

Assembly members:
C-type_lectin, polymer, 156 residues, 18610.879 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
C-type_lectin: MVCPIDWRAFQSNCYFPLTD NKTWAESERNCSGMGAHLMT ISTEAEQNFIIQFLDRRLSY FLGLRDENAKGQWRWVDQTP FNPRRVFWHKNEPDNSQGEN CVVLVYNQDKWAWNDVPCNF EASRICKIPGTTLNAENLYF QSHHHHHHWSHPQFEK

Data sets:
Data typeCount
13C chemical shifts673
15N chemical shifts169
1H chemical shifts1047

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1human C-type lectin domain family 4 member D1

Entities:

Entity 1, human C-type lectin domain family 4 member D 156 residues - 18610.879 Da.

expressed sequence start-stop 84-215 (156 aa incl tag) N-term cloning artifact MV- C-term cloning artifact -AENLYFQSHHHHHHWSHPQFEK Only residues 1-142 included in structure calculations

1   METVALCYSPROILEASPTRPARGALAPHE
2   GLNSERASNCYSTYRPHEPROLEUTHRASP
3   ASNLYSTHRTRPALAGLUSERGLUARGASN
4   CYSSERGLYMETGLYALAHISLEUMETTHR
5   ILESERTHRGLUALAGLUGLNASNPHEILE
6   ILEGLNPHELEUASPARGARGLEUSERTYR
7   PHELEUGLYLEUARGASPGLUASNALALYS
8   GLYGLNTRPARGTRPVALASPGLNTHRPRO
9   PHEASNPROARGARGVALPHETRPHISLYS
10   ASNGLUPROASPASNSERGLNGLYGLUASN
11   CYSVALVALLEUVALTYRASNGLNASPLYS
12   TRPALATRPASNASPVALPROCYSASNPHE
13   GLUALASERARGILECYSLYSILEPROGLY
14   THRTHRLEUASNALAGLUASNLEUTYRPHE
15   GLNSERHISHISHISHISHISHISTRPSER
16   HISPROGLNPHEGLULYS

Samples:

sample_1: C-type lectin, [U-13C; U-15N], 1 mM; sodium acetate 10 mM; EDTA 0.1 mM; H2O 90%; D2O 10%

sample_2: C-type lectin, [U-13C; U-15N], 1 mM; sodium acetate 10 mM; EDTA 0.1 mM; D2O 100%

sample_conditions_1: ionic strength: 10 mM; pH: 4.5; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
15N HSQCsample_1isotropicsample_conditions_1
15N NOESY-HSQCsample_1isotropicsample_conditions_1
13C CT-HSQCsample_2isotropicsample_conditions_1
aromatic 13C CT-HSQCsample_2isotropicsample_conditions_1
13C NOESY-HSQCsample_2isotropicsample_conditions_1
13C aromatic NOESY-HSQCsample_2isotropicsample_conditions_1
HNCOsample_1isotropicsample_conditions_1
HNCACOsample_1isotropicsample_conditions_1
HNCAsample_1isotropicsample_conditions_1
HNCOCAsample_1isotropicsample_conditions_1
HNCACBsample_1isotropicsample_conditions_1
CBCACONHsample_1isotropicsample_conditions_1

Software:

CCPN v2.1.5, CCPN - chemical shift assignment, peak picking

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

ARIA v2.3, Linge, O, . - structure solution

NMRPipe v5.4, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMRJ v2.2D, Varian - collection

TOPSPIN, Bruker Biospin - collection

MDDNMR v2.0, (MDDNMR) Orekhov, Jaravine, Kazimierczuk - collection, processing

MDDGUI v1.0, (MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmith - collection, processing

NMR spectrometers:

  • Varian Inova 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
GB AAH32313 AAL37713 AAM75389 AAQ63173 AAS59161
REF NP_525126 XP_001134875 XP_003265492 XP_003808712 XP_004052704
SP Q8WXI8

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts