BMRB Entry 34472

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34472
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Haddock model of NDM-1/myricetin complex
Deposition date:
2019-12-26
Original release date:
2021-01-06
Authors:
Riviere, G.; Oueslati, S.; Gayral, M.; Crechet, J.; Nhiri, N.; Jacquet, E.; Cintrat, J.; Giraud, F.; van Heijenoort, C.; Lescop, E.; Pethe, S.; Iorga, B.; Naas, T.; Guittet, E.; Morellet, N.
Citation:

Citation: Marra, A.. "NDM-1: a local clone emerges with worldwide aspirations."  Future Microbiol. 6, 137-141 (2011).
PubMed: 21366414

Assembly members:

Assembly members:
entity_1, polymer, 228 residues, 24032.010 Da.
entity_ZN, non-polymer, 65.409 Da.
entity_MYC, non-polymer, 318.235 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 573   Superkingdom: not available   Kingdom: not available   Genus/species: Klebsiella pneumoniae

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GDQRFGDLVFRQLAPNVWQH TSYLDMPGFGAVASNGLIVR DGGRVLVVDTAWTDDQTAQI LNWIKQEINLPVALAVVTHA HQDKMGGMDALHAAGIATYA NALSNQLAPQEGMVAAQHSL TFAANGWVEPATAPNFGPLK VFYPGPGHTSDNITVGIDGT DIAFGGCLIKDSKAKSLGNL GDADTEHYAASARAFGAAFP KASMIVMSHSAPDSRAAITH TARMADKL

Data sets:
Data typeCount
13C chemical shifts581
15N chemical shifts206
1H chemical shifts206

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_32
4unit_43

Entities:

Entity 1, unit_1 228 residues - 24032.010 Da.

1   GLYASPGLNARGPHEGLYASPLEUVALPHE
2   ARGGLNLEUALAPROASNVALTRPGLNHIS
3   THRSERTYRLEUASPMETPROGLYPHEGLY
4   ALAVALALASERASNGLYLEUILEVALARG
5   ASPGLYGLYARGVALLEUVALVALASPTHR
6   ALATRPTHRASPASPGLNTHRALAGLNILE
7   LEUASNTRPILELYSGLNGLUILEASNLEU
8   PROVALALALEUALAVALVALTHRHISALA
9   HISGLNASPLYSMETGLYGLYMETASPALA
10   LEUHISALAALAGLYILEALATHRTYRALA
11   ASNALALEUSERASNGLNLEUALAPROGLN
12   GLUGLYMETVALALAALAGLNHISSERLEU
13   THRPHEALAALAASNGLYTRPVALGLUPRO
14   ALATHRALAPROASNPHEGLYPROLEULYS
15   VALPHETYRPROGLYPROGLYHISTHRSER
16   ASPASNILETHRVALGLYILEASPGLYTHR
17   ASPILEALAPHEGLYGLYCYSLEUILELYS
18   ASPSERLYSALALYSSERLEUGLYASNLEU
19   GLYASPALAASPTHRGLUHISTYRALAALA
20   SERALAARGALAPHEGLYALAALAPHEPRO
21   LYSALASERMETILEVALMETSERHISSER
22   ALAPROASPSERARGALAALAILETHRHIS
23   THRALAARGMETALAASPLYSLEU

Entity 2, unit_2 - Zn - 65.409 Da.

1   ZN

Entity 3, unit_4 - C15 H10 O8 - 318.235 Da.

1   MYC

Samples:

sample_1: NDM-1, [U-13C; U-15N], 320 uM

sample_conditions_1: ionic strength: 150 mM; pH: 7; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
HNCACOsample_1isotropicsample_conditions_1
HNCOCACBsample_1isotropicsample_conditions_1
HNCOCAsample_1isotropicsample_conditions_1

Software:

TopSpin v3.5, Bruker Biospin - collection

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

HADDOCK, Bonvin - structure calculation

NMR spectrometers:

  • Bruker AVANCE II 600 MHz
  • Bruker AVANCE III 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks