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- PDB-5ev8: Crystal structure of the metallo-beta-lactamase IMP-1 in complex ... -

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Basic information

Entry
Database: PDB / ID: 5ev8
TitleCrystal structure of the metallo-beta-lactamase IMP-1 in complex with the bisthiazolidine inhibitor D-CS319
ComponentsBeta-lactamase IMP-1
KeywordsHYDROLASE / inhibitor / carbapenemase / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3R9 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI100560 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Cross-class metallo-beta-lactamase inhibition by bisthiazolidines reveals multiple binding modes.
Authors: Hinchliffe, P. / Gonzalez, M.M. / Mojica, M.F. / Gonzalez, J.M. / Castillo, V. / Saiz, C. / Kosmopoulou, M. / Tooke, C.L. / Llarrull, L.I. / Mahler, G. / Bonomo, R.A. / Vila, A.J. / Spencer, J.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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
Revision 1.3Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase IMP-1
B: Beta-lactamase IMP-1
C: Beta-lactamase IMP-1
D: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,43926
Polymers101,2034
Non-polymers2,23522
Water5,170287
1
A: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9065
Polymers25,3011
Non-polymers6064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9338
Polymers25,3011
Non-polymers6337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8688
Polymers25,3011
Non-polymers5677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7315
Polymers25,3011
Non-polymers4304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.560, 77.713, 261.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase IMP-1 / BLAIMP / Beta-lactamase type II / Penicillinase


Mass: 25300.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): solu / References: UniProt: P52699, beta-lactamase

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Non-polymers , 7 types, 309 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-3R9 / (3S,5S,7aR)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid


Mass: 237.363 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H11NO2S3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium acetate, 25% PEG 8000. 1ul protein (25 mg/ml) mixed with 1ul reagent

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.3→37.24 Å / Num. obs: 45125 / % possible obs: 100 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 18.1 % / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDK

1ddk


Resolution: 2.3→37.238 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 2206 4.89 %
Rwork0.1777 --
obs0.1798 45120 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6873 0 103 287 7263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097159
X-RAY DIFFRACTIONf_angle_d1.1789712
X-RAY DIFFRACTIONf_dihedral_angle_d12.3632576
X-RAY DIFFRACTIONf_chiral_restr0.051081
X-RAY DIFFRACTIONf_plane_restr0.0061207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.31190.24062647X-RAY DIFFRACTION100
2.35-2.40470.26531350.22152624X-RAY DIFFRACTION100
2.4047-2.46480.27211620.21082610X-RAY DIFFRACTION100
2.4648-2.53140.31761360.20942634X-RAY DIFFRACTION100
2.5314-2.60590.27621380.20082635X-RAY DIFFRACTION100
2.6059-2.690.2411340.20462682X-RAY DIFFRACTION100
2.69-2.78610.26021370.20082628X-RAY DIFFRACTION100
2.7861-2.89760.25791460.20372650X-RAY DIFFRACTION100
2.8976-3.02940.24361500.19362655X-RAY DIFFRACTION100
3.0294-3.18910.22271150.18422681X-RAY DIFFRACTION100
3.1891-3.38870.23751330.17962674X-RAY DIFFRACTION100
3.3887-3.65020.22261370.17652696X-RAY DIFFRACTION100
3.6502-4.01710.19371400.17122709X-RAY DIFFRACTION100
4.0171-4.59750.20611350.15392723X-RAY DIFFRACTION100
4.5975-5.78890.17511430.15472749X-RAY DIFFRACTION100
5.7889-37.24330.18511460.15532917X-RAY DIFFRACTION100

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