BMRB Entry 15315

Name: Resonance assignments for the discoidin domain of DDR2.
Published: 2008-02-29

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PDB ID: 2z4f
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15315
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Resonance assignments for the discoidin domain of DDR2.

Deposition date:

2007-06-19

Original release date:

2008-02-29

Authors:

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

Citation:

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).
PubMed: 17703188

Assembly members:

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

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	633
15N chemical shifts	166
1H chemical shifts	1069

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DDR2-DS	1

Entities:

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

1

ASN

PRO

ALA

ILE

CYS

ARG

TYR

PRO

LEU

GLY

2

MET

SER

GLY

GLN

ILE

PRO

ASP

GLU

ASP

3

ILE

THR

ALA

SER

GLN

TRP

SER

GLU

SER

4

THR

ALA

LYS

TYR

GLY

ARG

LEU

ASP

SER

5

GLU

GLY

ASP

GLY

ALA

TRP

CYS

PRO

GLU

6

ILE

PRO

VAL

GLU

PRO

ASP

LEU

LYS

GLU

7

PHE

LEU

GLN

ILE

ASP

LEU

HIS

THR

LEU

HIS

8

PHE

ILE

THR

LEU

VAL

GLY

THR

GLN

GLY

ARG

9

HIS

ALA

GLY

HIS

GLY

ILE

GLU

PHE

ALA

10

PRO

MET

TYR

LYS

ILE

ASN

TYR

SER

ARG

ASP

11

GLY

THR

ARG

TRP

ILE

SER

TRP

ARG

ASN

ARG

12

HIS

GLY

LYS

GLN

VAL

LEU

ASP

GLY

ASN

SER

13

ASN

PRO

TYR

ASP

ILE

PHE

LEU

LYS

ASP

LEU

14

GLU

PRO

ILE

VAL

ALA

ARG

PHE

VAL

ARG

15

PHE

ILE

PRO

VAL

THR

ASP

HIS

SER

MET

ASN

16

VAL

CYS

MET

ARG

VAL

GLU

LEU

TYR

GLY

CYS

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_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

PDB	2WUH 2Z4F
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
AlphaFold	Q16832