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- PDB-6ovz: Crystal structure of the New Delhi metallo-beta-lactamase-1 adduc... -

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Basic information

Entry
Database: PDB / ID: 6ovz
TitleCrystal structure of the New Delhi metallo-beta-lactamase-1 adduct with a lysine-targeted affinity label
Components(Beta-lactamase) x 2
KeywordsHYDROLASE / NDM-1 / affinity-label / covalent inhibitor
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / 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
benzyl hydroxycarbamate / benzyl (carboxyoxy)carbamate / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.017 Å
AuthorsMonzingo, A.F. / Fast, W. / Thomas, P.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111926 United States
CitationJournal: Biochemistry / Year: 2019
Title: A Lysine-Targeted Affinity Label for Serine-beta-Lactamase Also Covalently Modifies New Delhi Metallo-beta-lactamase-1 (NDM-1).
Authors: Thomas, P.W. / Cammarata, M. / Brodbelt, J.S. / Monzingo, A.F. / Pratt, R.F. / Fast, W.
History
DepositionMay 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0May 17, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _cell.Z_PDB / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id / _struct_ref_seq.ref_id / _struct_site.pdbx_num_residues
Revision 2.1Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,62212
Polymers49,7712
Non-polymers85110
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-231 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.023, 73.903, 145.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Beta-lactamase / BlaNDM-1 / BlaNDM-1 metallo beta lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase NDM-1 ...BlaNDM-1 / BlaNDM-1 metallo beta lactamase / Metallo-beta-lactamase / Metallo-beta-lactamase NDM-1 / NDM-1 / NDM-1 metallo-beta-lactamase / New Delhi metallo-beta-lactamase NDM-1 / Subclass B1 metallo-beta-lactamase / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 24863.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaNDM-1, bla NDM-1, APU18_05360, AZ95_0035, BANRA_05542, BET08_16280, BVL39_26630, C0R28_25820, C6985_28190, D3O91_26550, DWB25_28700, ECS01_0033, EOL26_24905, MS6198_A142, NDM1Dok01_N0175, ...Gene: blaNDM-1, bla NDM-1, APU18_05360, AZ95_0035, BANRA_05542, BET08_16280, BVL39_26630, C0R28_25820, C6985_28190, D3O91_26550, DWB25_28700, ECS01_0033, EOL26_24905, MS6198_A142, NDM1Dok01_N0175, pNDM102337_147, pNDM10505_149
Plasmid: pet27b-strep-NDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E5KIY2
#2: Protein Beta-lactamase / Beta-lactamase NDM-1 / BlaNDM-1 / BlaNDM-1 metallo beta lactamase / Metallo-beta-lactamase / NDM-1 ...Beta-lactamase NDM-1 / BlaNDM-1 / BlaNDM-1 metallo beta lactamase / Metallo-beta-lactamase / NDM-1 / NDM-1 metallo-beta-lactamase / New Delhi metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamase-1 / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 24906.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaNDM-1, bla NDM-1, A9X72_27270, AZ95_0035, BANRA_05542, E4K51_24975, ECS01_0033, G5603_25730, G9448_24155, NDM1Dok01_N0175, pNDM102337_147, pNDM10505_149
Plasmid: pet27b-strep-NDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E5KIY2

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Non-polymers , 5 types, 231 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-N9M / benzyl (carboxyoxy)carbamate


Mass: 211.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-N9J / benzyl hydroxycarbamate


Mass: 167.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M calcium chloride dihydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014
RadiationMonochromator: single crystal, cylindrically bent, Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.017→50 Å / Num. obs: 28507 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 19.76 Å2 / Rmerge(I) obs: 0.126 / Χ2: 1.01 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.017-2.055.60.54514080.557198.1
2.05-2.096.40.49813740.591199.3
2.09-2.137.10.44413810.601199.6
2.13-2.187.20.38314090.655199.6
2.18-2.227.30.34213750.663199.8
2.22-2.277.20.31714160.701199.7
2.27-2.337.30.30814150.703199.8
2.33-2.397.20.28914010.72199.7
2.39-2.477.30.25714070.762199.9
2.47-2.547.30.22414020.799199.9
2.54-2.647.20.20614170.851100
2.64-2.747.20.1714140.9051100
2.74-2.877.20.15714060.9761100
2.87-3.027.20.13114481.0371100
3.02-3.217.20.11214121.2081100
3.21-3.457.10.0914351.3961100
3.45-3.870.07914451.6251100
3.8-4.356.80.07514751.921100
4.35-5.486.70.06314751.6851100
5.48-506.40.05715921.714199.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s0z

3s0z


Resolution: 2.017→40.564 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2305 1385 5.04 %
Rwork0.1833 --
obs0.1857 27482 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.98 Å2 / Biso mean: 19.1601 Å2 / Biso min: 7.68 Å2
Refinement stepCycle: final / Resolution: 2.017→40.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 37 221 3572
Biso mean--34.08 21.35 -
Num. residues----454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0165-2.08860.27281050.20212267237285
2.0886-2.17220.27551370.1962524266193
2.1722-2.27110.25881650.18392494265995
2.2711-2.39080.2971330.19182559269295
2.3908-2.54050.22731400.19542568270896
2.5405-2.73670.26861290.19722643277298
2.7367-3.0120.29981220.20282700282298
3.012-3.44760.24291380.18742685282399
3.4476-4.34290.17711620.160527632925100
4.3429-40.57260.18571540.170628943048100

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