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BMRB: 34472

8GPC

Haddock model of NDM-1/myricetin complex

Authors

Riviere, G., Oueslati, S., Gayral, M., Crechet, J.B., Nhiri, N., Jacquet, E., Cintrat, J.C., Giraud, F., van Heijenoort, C., Lescop, E., Pethe, S., Iorga, B.I., Naas, T., Guittet, E., Morellet, N.

Assembly

Metallo beta lactamase NDM-1

Entity

1. Metallo beta lactamase NDM-1, entity 1 (polymer, Thiol state: all other bound), 228 monomers, 24007.77 Da Detail

GDQRFGDLVF RQLAPNVWQH TSYLDMPGFG AVASNGLIVR DGGRVLVVDT AWTDDQTAQI LNWIKQEINL PVALAVVTHA HQDKMGGMDA LHAAGIATYA NALSNQLAPQ EGMVAAQHSL TFAANGWVEP ATAPNFGPLK VFYPGPGHTS DNITVGIDGT DIAFGGCLIK DSKAKSLGNL GDADTEHYAA SARAFGAAFP KASMIVMSHS APDSRAAITH TARMADKL

2. Metallo beta lactamase NDM-1, entity ZN (non-polymer), 65.409 × 2 Da
3. Metallo beta lactamase NDM-1, entity MYC (non-polymer), 318.235 Da

Total weight

24456.822 Da

Max. entity weight

24007.77 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS79:NE2	2:ZN1:ZN
2	na	sing	1:HIS81:ND1	2:ZN1:ZN
3	na	sing	1:ASP83:OD1	2:ZN1:ZN
4	na	sing	1:HIS209:NE2	2:ZN1:ZN
5	na	sing	2:ZN1:ZN	3:MYC1:O30

Source organism

Klebsiella pneumoniae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 41.3 %, Completeness (bb): 74.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	41.3 % (1027 of 2486)	18.2 % (230 of 1261)	60.4 % (590 of 977)	83.5 % (207 of 248)
Backbone	74.2 % (999 of 1346)	45.2 % (211 of 467)	87.9 % (582 of 662)	94.9 % (206 of 217)
Sidechain	14.1 % (190 of 1346)	2.4 % (19 of 794)	32.6 % (170 of 521)	3.2 % (1 of 31)
Aromatic	0.0 % (0 of 206)	0.0 % (0 of 103)	0.0 % (0 of 99)	0.0 % (0 of 4)
Methyl	17.6 % (48 of 272)	5.9 % (8 of 136)	29.4 % (40 of 136)

1. entity 1

GDQRFGDLVF RQLAPNVWQH TSYLDMPGFG AVASNGLIVR DGGRVLVVDT AWTDDQTAQI LNWIKQEINL PVALAVVTHA HQDKMGGMDA LHAAGIATYA NALSNQLAPQ EGMVAAQHSL TFAANGWVEP ATAPNFGPLK VFYPGPGHTS DNITVGIDGT DIAFGGCLIK DSKAKSLGNL GDADTEHYAA SARAFGAAFP KASMIVMSHS APDSRAAITH TARMADKL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NDM-1	[U-13C; U-15N]		320 uM

Protein Blocks Logo

Calculated from 4 models in PDB: 6TTC, Strand ID: A Detail

Release date

2020-07-13

Citation

NDM-1: a local clone emerges with worldwide aspirations
Marra, A.
Future Microbiol. (2011), 6, 137-141, PubMed 21366414 , DOI 10.2217/fmb.10.171 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34471 released on 2020-07-13
Title Haddock model of NDM-1/morin complex

Related entities 1. Metallo beta lactamase NDM-1, entity 1, : 1 : 100 : 14 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE II - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NDM-1	[U-13C; U-15N]		320 uM

2 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NDM-1	[U-13C; U-15N]		320 uM

3 3D HNCO

Instrument

Bruker AVANCE II - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NDM-1	[U-13C; U-15N]		320 uM

4 3D HNCA

Instrument

Bruker AVANCE II - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NDM-1	[U-13C; U-15N]		320 uM

5 3D HNCACB

Instrument

Bruker AVANCE II - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NDM-1	[U-13C; U-15N]		320 uM

6 HNCACO

Instrument

Bruker AVANCE II - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NDM-1	[U-13C; U-15N]		320 uM

7 HNCOCACB

Instrument

Bruker AVANCE II - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NDM-1	[U-13C; U-15N]		320 uM

8 HNCOCA

Instrument

Bruker AVANCE II - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 320 uM [U-13C; U-15N] NDM-1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	NDM-1	[U-13C; U-15N]		320 uM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34472_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:79:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:81:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:83:ASP:OD1	2:1:ZN:ZN	unknown	unknown	n/a
1:209:HIS:NE2	3:1:ZN:ZN	unknown	unknown	n/a
2:1:ZN:ZN	4:1:MYC:O30	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr34472_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	993		97.4 (chain: 1, length: 228)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 228, Sequence coverage: 97.4%
- Total number of assignments
  - ¹³C chemical shifts: 581
  - ¹H chemical shifts: 206
  - ¹⁵N chemical shifts: 206
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords Haddock, METAL BINDING PROTEIN, Myricetin, New-Delhi Metallo-beta-lactamase-1, antimicrobial resistance, complex, inhibitor