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- PDB-6xci: Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-3D -

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Basic information

Entry
Database: PDB / ID: 6xci
TitleStructure of NDM-1 in complex with macrocycle inhibitor NDM1i-3D
Components
  • BlaNDM-4_1_JQ348841
  • Macrocycle NDM1i-3D
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Cyclic peptide / macrocycle inhibitor / ANTIBIOTIC / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


beta-lactamase activity / beta-lactamase
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 / ACETATE ION / : / polypeptide(D) / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: BlaNDM-4_1_JQ348841
A: BlaNDM-4_1_JQ348841
H: Macrocycle NDM1i-3D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,16210
Polymers53,5223
Non-polymers6407
Water6,413356
1
B: BlaNDM-4_1_JQ348841
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7356
Polymers26,2741
Non-polymers4625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-55 kcal/mol
Surface area9230 Å2
MethodPISA
2
A: BlaNDM-4_1_JQ348841
H: Macrocycle NDM1i-3D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4274
Polymers27,2492
Non-polymers1782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-63 kcal/mol
Surface area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.168, 73.789, 77.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 42 - 269 / Label seq-ID: 20 - 247

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

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Protein / Polypeptide(D) , 2 types, 3 molecules BAH

#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.: 2
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: Polypeptide(D) Macrocycle NDM1i-3D


Type: Cyclic peptide / Class: Inhibitor / Mass: 975.162 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Macrocycle / cyclic peptide sequence: D-cysteine Proline 2-aminomethyl-L-phenylalanine (LWI cif) Hydroxyproline Glutamate D-proline D-lysine Norleucine
Source: (synth.) synthetic construct (others) / References: Inhibitor, Cyclic peptide

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Non-polymers , 4 types, 363 molecules

#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 36.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% 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: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.6→42.8 Å / Num. obs: 49546 / % possible obs: 90.6 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 19.9
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
1.6-1.631.40.37711248310.7970.3370.5072.131.2
8.76-42.765.80.03523054000.9990.0150.03840.699.4

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Processing

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

4exs


Resolution: 1.6→42.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.334 / SU ML: 0.046 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1598 2688 5.4 %RANDOM
Rwork0.1368 ---
obs0.1381 46797 90.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.93 Å2 / Biso mean: 14.539 Å2 / Biso min: 4.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å2-0 Å2
2---0.49 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.6→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 9 356 3782
Biso mean--23.6 25.59 -
Num. residues----461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133545
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173230
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.6334839
X-RAY DIFFRACTIONr_angle_other_deg1.5711.587497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7145473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5123.395162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60315522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4621514
X-RAY DIFFRACTIONr_chiral_restr0.0860.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024078
Refine LS restraints NCS

Ens-ID: 1 / Number: 7073 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.601→1.643 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 82 -
Rwork0.218 1315 -
all-1397 -
obs--35.15 %

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