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- PDB-6r73: Structure of IMP-13 metallo-beta-lactamase complexed with hydroly... -

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Basic information

Entry
Database: PDB / ID: 6r73
TitleStructure of IMP-13 metallo-beta-lactamase complexed with hydrolysed meropenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / Metallo-Beta-Lactamase / Zinc-binding protein / 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 / : / 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
Chem-LMP / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSoftley, C.A. / Zak, K. / Kolonko, M. / Sattler, M. / Popowicz, G.
Funding support Germany, Poland, 3items
OrganizationGrant numberCountry
European Union675555 Germany
German Federal Ministry for Education and ResearchGFPARV38 Germany
Polish National Science Centre2018/28T/NZ1/00337 Poland
CitationJournal: Antimicrob.Agents Chemother. / Year: 2020
Title: Structure and Molecular Recognition Mechanism of IMP-13 Metallo-beta-Lactamase.
Authors: Softley, C.A. / Zak, K.M. / Bostock, M.J. / Fino, R. / Zhou, R.X. / Kolonko, M. / Mejdi-Nitiu, R. / Meyer, H. / Sattler, M. / Popowicz, G.M.
History
DepositionMar 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 3, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)51,2868
Polymers50,2212
Non-polymers1,0656
Water1,76598
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6434
Polymers25,1111
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6434
Polymers25,1111
Non-polymers5323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.979, 72.368, 61.194
Angle α, β, γ (deg.)90.00, 108.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 25110.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla-imp13, bla-IMP13, blaIMP-13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7WYA8, beta-lactamase
#2: Chemical ChemComp-LMP / (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoy l)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Hydrolyzed Meropenem


Mass: 401.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 25% PEG 3350, cryo-protected with MPD

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9765 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 9, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.3→58.04 Å / Num. obs: 20856 / % possible obs: 97.01 % / Redundancy: 1.9 % / Biso Wilson estimate: 33.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.06752 / Net I/σ(I): 7.62
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 2130 / CC1/2: 0.84 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DD6

1dd6


Resolution: 2.3→58.04 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.51
RfactorNum. reflection% reflection
Rfree0.2481 1081 5.19 %
Rwork0.1887 --
obs0.1918 20826 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→58.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 58 98 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073441
X-RAY DIFFRACTIONf_angle_d0.9934697
X-RAY DIFFRACTIONf_dihedral_angle_d5.9122651
X-RAY DIFFRACTIONf_chiral_restr0.074535
X-RAY DIFFRACTIONf_plane_restr0.005582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40470.3831380.27962513X-RAY DIFFRACTION99
2.4047-2.53150.3191240.2692510X-RAY DIFFRACTION99
2.5315-2.69010.33571460.23392512X-RAY DIFFRACTION99
2.6901-2.89780.31461320.21452547X-RAY DIFFRACTION99
2.8978-3.18940.26941370.18912497X-RAY DIFFRACTION99
3.1894-3.65080.20891460.16522493X-RAY DIFFRACTION99
3.6508-4.59940.18871000.15182150X-RAY DIFFRACTION89
4.5994-58.06140.21411580.17012523X-RAY DIFFRACTION98

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