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- PDB-6xbe: Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-1F -

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Basic information

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


antibiotic catabolic process / beta-lactamase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Inhibitor, Cyclic peptide / NDM-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,76420
Polymers108,9798
Non-polymers78512
Water8,179454
1
A: BlaNDM-4_1_JQ348841
F: macrocycle inhibitor NDM1i-1F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4415
Polymers27,2452
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-112 kcal/mol
Surface area9930 Å2
MethodPISA
2
B: BlaNDM-4_1_JQ348841
G: macrocycle inhibitor NDM1i-1F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5066
Polymers27,2452
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-113 kcal/mol
Surface area9900 Å2
MethodPISA
3
C: BlaNDM-4_1_JQ348841
H: macrocycle inhibitor NDM1i-1F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3764
Polymers27,2452
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-114 kcal/mol
Surface area9890 Å2
MethodPISA
4
D: BlaNDM-4_1_JQ348841
I: macrocycle inhibitor NDM1i-1F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4415
Polymers27,2452
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-114 kcal/mol
Surface area9800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.699, 74.551, 77.310
Angle α, β, γ (deg.)96.520, 103.110, 106.240
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

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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-1F


Type: Cyclic peptide / Class: Inhibitor / Mass: 971.178 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: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.68 %
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

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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: 1.8→46.76 Å / Num. obs: 72645 / % possible obs: 89.5 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.052 / Rrim(I) all: 0.079 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.841.50.876365323800.5420.8421.2170.749.4
9-46.7220.02912166150.9960.0260.03922.793.5

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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: 1.8→46.76 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.888 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 3632 5 %RANDOM
Rwork0.1848 ---
obs0.1867 69009 89.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.94 Å2 / Biso mean: 35.189 Å2 / Biso min: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.02 Å20.73 Å2
2---0.66 Å2-2.7 Å2
3---1.33 Å2
Refinement stepCycle: final / Resolution: 1.8→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7015 0 12 466 7493
Biso mean--29.44 40.55 -
Num. residues----948
Refine LS restraintsType: r_bond_refined_d / Dev ideal: 0.007 / Dev ideal target: 0.013 / Number: 7238
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A75350.05
12B75350.05
21A73970.07
22C73970.07
31A74400.07
32D74400.07
41B75450.07
42C75450.07
51B75250.07
52D75250.07
61C74720.06
62D74720.06
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 153 -
Rwork0.376 2916 -
all-3069 -
obs--51 %

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