BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 15315

Title: Resonance assignments for the discoidin domain of DDR2.   PubMed: 17703188

Authors: Ichikawa, Osamu; Osawa, Masonori; Nishida, Noritaka; Goshima, Naoki; Nomura, Nobuo; Shimada, Ichio

Citation: Ichikawa, Osamu; Osawa, Masonori; Nishida, Noritaka; Goshima, Naoki; Nomura, Nobuo; Shimada, Ichio. "Structural basis of the collagen-binding mode of discoidin domain receptor 2"  EMBO J. 26, 4168-4176 (2007).

Assembly members:
DDR2-DS, polymer, 161 residues, Formula weight is not available

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

Experimental source:   Production method: recombinant technology   Host organism: Pichia pastoris

Entity Sequences (FASTA):
DDR2-DS: NPAICRYPLGMSGGQIPDED ITASSQWSESTAAKYGRLDS EEGDGAWCPEIPVEPDDLKE FLQIDLHTLHFITLVGTQGR HAGGHGIEFAPMYKINYSRD GTRWISWRNRHGKQVLDGNS NPYDIFLKDLEPPIVARFVR FIPVTDHSMNVCMRVELYGC V

Data sets:
Data typeCount
13C chemical shifts633
15N chemical shifts166
1H chemical shifts1069

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DDR2-DS1

Entities:

Entity 1, DDR2-DS 161 residues - Formula weight is not available

1   ASNPROALAILECYSARGTYRPROLEUGLY
2   METSERGLYGLYGLNILEPROASPGLUASP
3   ILETHRALASERSERGLNTRPSERGLUSER
4   THRALAALALYSTYRGLYARGLEUASPSER
5   GLUGLUGLYASPGLYALATRPCYSPROGLU
6   ILEPROVALGLUPROASPASPLEULYSGLU
7   PHELEUGLNILEASPLEUHISTHRLEUHIS
8   PHEILETHRLEUVALGLYTHRGLNGLYARG
9   HISALAGLYGLYHISGLYILEGLUPHEALA
10   PROMETTYRLYSILEASNTYRSERARGASP
11   GLYTHRARGTRPILESERTRPARGASNARG
12   HISGLYLYSGLNVALLEUASPGLYASNSER
13   ASNPROTYRASPILEPHELEULYSASPLEU
14   GLUPROPROILEVALALAARGPHEVALARG
15   PHEILEPROVALTHRASPHISSERMETASN
16   VALCYSMETARGVALGLULEUTYRGLYCYS
17   VAL

Samples:

sample_1: DDR2-DS, [U-98% 13C; U-98% 15N], 0.4 mM; PHOSHATE BUFFER 10 mM; NACL 100 mM; H2O 95%; D2O 5%

sample_2: DDR2-DS, [U-98% 13C; U-98% 15N], 0.4 mM; PHOSHATE BUFFER 10 mM; NACL 100 mM; D2O 5%

sample_3: DDR2-DS, [U-98% 15N], 0.4 mM; PHOSHATE BUFFER 10 mM; NACL 100 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.1 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HNHAsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-15N TOCSYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1

Software:

xwinnmr, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAG37013 BAG53183
EMBL CAA52777 CAE45946
GB AAH52998 AAI34427 ACE86808 ACE87495 EAW90713
REF NP_001014796 NP_001077189 NP_006173 XP_001118219 XP_001174340
SP Q16832
TPG DAA31987