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- PDB-6ibs: Crystal structure of NDM-1 beta-lactamase in complex with boronic... -

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Basic information

Entry
Database: PDB / ID: 6ibs
TitleCrystal structure of NDM-1 beta-lactamase in complex with boronic inhibitor cpd 6
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / beta-lactamase / bacterial resistance / acyclic boronic inhibitors
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HB8 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsMaso, L. / Quotadamo, A. / Bellio, P. / Montanari, M. / Venturelli, A. / Celenza, G. / Costi, M.P. / Tondi, D. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme286998 Italy
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: X-ray Crystallography Deciphers the Activity of Broad-Spectrum Boronic Acid beta-Lactamase Inhibitors.
Authors: Cendron, L. / Quotadamo, A. / Maso, L. / Bellio, P. / Montanari, M. / Celenza, G. / Venturelli, A. / Costi, M.P. / Tondi, D.
History
DepositionNov 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,76312
Polymers51,7202
Non-polymers1,04210
Water6,666370
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3816
Polymers25,8601
Non-polymers5215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3816
Polymers25,8601
Non-polymers5215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.285, 73.737, 77.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 25860.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The electron density maps allow the reconstruction of these residues only. Those missing are unobserved regions
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HB8 / [7-[(2-methylpropan-2-yl)oxycarbonylamino]-1-benzothiophen-2-yl]-tris(oxidanyl)boranuide


Mass: 310.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17BNO5S
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→42.59 Å / Num. obs: 83133 / % possible obs: 97.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.026 / Net I/σ(I): 20.3
Reflection shellResolution: 1.37→1.419 Å / Rmerge(I) obs: 0.488 / Num. unique obs: 4061 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZGU

5zgu


Resolution: 1.37→42.59 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.825 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16334 3717 4.5 %RANDOM
Rwork0.13225 ---
obs0.13367 79355 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.042 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å2-0 Å2
2---1.07 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.37→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 50 370 3786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0143644
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173223
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.6614990
X-RAY DIFFRACTIONr_angle_other_deg1.1871.6567533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83122.921178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37715552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9281519
X-RAY DIFFRACTIONr_chiral_restr0.1120.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024266
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02685
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_mcbond_it2.0791.1551881
X-RAY DIFFRACTIONr_mcbond_other2.0651.1511879
X-RAY DIFFRACTIONr_mcangle_it2.3931.732367
X-RAY DIFFRACTIONr_mcangle_other2.3921.7322368
X-RAY DIFFRACTIONr_scbond_it4.181.4791763
X-RAY DIFFRACTIONr_scbond_other4.1791.4791764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5322.1052617
X-RAY DIFFRACTIONr_long_range_B_refined3.73915.2234175
X-RAY DIFFRACTIONr_long_range_B_other3.60814.8144101
X-RAY DIFFRACTIONr_rigid_bond_restr5.91236867
X-RAY DIFFRACTIONr_sphericity_free22.1315248
X-RAY DIFFRACTIONr_sphericity_bonded13.40556906
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.557 144 -
Rwork0.52 5895 -
obs--96.69 %

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