[English] 日本語
Yorodumi
- PDB-6xbf: Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-1G -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xbf
TitleStructure of NDM-1 in complex with macrocycle inhibitor NDM1i-1G
Components
  • BlaNDM-4_1_JQ348841
  • macrocycle inhibitor NDM1i-1G
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Cyclic peptide / macrocycle inhibitor / ANTIBIOTIC / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Inhibitor, Cyclic peptide / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWorrall, L.J. / Sun, T. / Mulligan, V.K. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Computationally designed peptide macrocycle inhibitors of New Delhi metallo-beta-lactamase 1.
Authors: Mulligan, V.K. / Workman, S. / Sun, T. / Rettie, S. / Li, X. / Worrall, L.J. / Craven, T.W. / King, D.T. / Hosseinzadeh, P. / Watkins, A.M. / Renfrew, P.D. / Guffy, S. / Labonte, J.W. / ...Authors: Mulligan, V.K. / Workman, S. / Sun, T. / Rettie, S. / Li, X. / Worrall, L.J. / Craven, T.W. / King, D.T. / Hosseinzadeh, P. / Watkins, A.M. / Renfrew, P.D. / Guffy, S. / Labonte, J.W. / Moretti, R. / Bonneau, R. / Strynadka, N.C.J. / Baker, D.
History
DepositionJun 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BlaNDM-4_1_JQ348841
F: macrocycle inhibitor NDM1i-1G
B: BlaNDM-4_1_JQ348841
G: macrocycle inhibitor NDM1i-1G
C: BlaNDM-4_1_JQ348841
H: macrocycle inhibitor NDM1i-1G
D: BlaNDM-4_1_JQ348841
I: macrocycle inhibitor NDM1i-1G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,82020
Polymers109,0358
Non-polymers78512
Water6,810378
1
A: BlaNDM-4_1_JQ348841
F: macrocycle inhibitor NDM1i-1G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4555
Polymers27,2592
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-115 kcal/mol
Surface area9920 Å2
MethodPISA
2
B: BlaNDM-4_1_JQ348841
G: macrocycle inhibitor NDM1i-1G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5206
Polymers27,2592
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-112 kcal/mol
Surface area9880 Å2
MethodPISA
3
C: BlaNDM-4_1_JQ348841
H: macrocycle inhibitor NDM1i-1G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3904
Polymers27,2592
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-112 kcal/mol
Surface area9850 Å2
MethodPISA
4
D: BlaNDM-4_1_JQ348841
I: macrocycle inhibitor NDM1i-1G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4555
Polymers27,2592
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-114 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.615, 74.190, 76.650
Angle α, β, γ (deg.)95.750, 103.460, 106.430
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A42 - 1008
2010B42 - 1008
1020A42 - 1008
2020C42 - 1008
1030A42 - 1008
2030D42 - 1008
1040B42 - 1008
2040C42 - 1008
1050B42 - 1008
2050D42 - 1008
1060C42 - 1008
2060D42 - 1008

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
BlaNDM-4_1_JQ348841 / Metallo beta-lactamase / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase / NDM-1 / NDM1 ...Metallo beta-lactamase / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase / NDM-1 / NDM1 metallo-beta-lactamase / New Delhi Metallo carbapenemase-1 / New Delhi metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamse 1


Mass: 26273.607 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: NDM-1, bla NDM-1, blaNDM-1, blaNDM1 / Production host: Escherichia coli (E. coli) / References: UniProt: E9NWK5
#2: Protein/peptide
macrocycle inhibitor NDM1i-1G


Type: Cyclic peptide / Class: Inhibitor / Mass: 985.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Inhibitor, Cyclic peptide
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) PEG 2000 monomethyl ether, 0.1M MES, pH 6.5 and 200mM NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→46.71 Å / Num. obs: 41538 / % possible obs: 94.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.798 / Num. unique obs: 3472 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EXS

4exs


Resolution: 2.2→46.71 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.204 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2077 5 %RANDOM
Rwork0.194 ---
obs0.197 39451 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.82 Å2 / Biso mean: 45.6 Å2 / Biso min: 8.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20.38 Å21.55 Å2
2---0.76 Å2-1.81 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 2.2→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7016 0 12 386 7414
Biso mean--42.61 46.37 -
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137216
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176542
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.639840
X-RAY DIFFRACTIONr_angle_other_deg1.2791.57315155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8025953
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54622.798336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.817151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2461533
X-RAY DIFFRACTIONr_chiral_restr0.0640.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028319
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A74690.07
12B74690.07
21A73550.07
22C73550.07
31A74030.08
32D74030.08
41B74010.08
42C74010.08
51B74320.07
52D74320.07
61C74140.08
62D74140.08
LS refinement shellResolution: 2.2→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 150 -
Rwork0.35 2830 -
all-2980 -
obs--91.66 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more