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

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Basic information

Entry
Database: PDB / ID: 6rzs
TitleStructure of IMP-13 metallo-beta-lactamase complexed with hydrolysed ertapenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / metallo-beta-lactamase
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; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
hydrolysed ertapenem / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsZak, K.M. / Softley, C. / Kolonko, M. / Sattler, M. / Popowicz, G.M.
Funding support Germany, Poland, 3items
OrganizationGrant numberCountry
European Union675555 Germany
German Federal Ministry for Education and ResearchGFTARV38 Germany
Polish National Science Centre2018/28/T/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
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 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 1.3Jun 3, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Jan 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id

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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)51,5848
Polymers50,3352
Non-polymers1,2496
Water3,675204
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7924
Polymers25,1681
Non-polymers6243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7924
Polymers25,1681
Non-polymers6243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.688, 48.105, 92.574
Angle α, β, γ (deg.)90.000, 105.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 25167.586 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 (E. coli) / References: UniProt: Q7WYA8, beta-lactamase
#2: Chemical ChemComp-LHT / hydrolysed ertapenem


Mass: 493.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N3O8S / 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.: 204 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M tri-Sodium acetate pH 5.6, 0.2 M Ammonium acetate, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→18.82 Å / Num. obs: 23338 / % possible obs: 97.8 % / Redundancy: 3.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.151 / Net I/σ(I): 6.6 / Num. measured all: 77735 / Scaling rejects: 367
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.2 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.2-2.261.002618519380.3971.994.7
9.06-18.820.05410443260.99516.588.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.36 Å18.82 Å
Translation4.36 Å18.82 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R78

6r78


Resolution: 2.2→18.82 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.219
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 1064 4.6 %RANDOM
Rwork0.2001 ---
obs0.2017 22254 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.96 Å2 / Biso mean: 37.358 Å2 / Biso min: 14.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20.86 Å2
2---1.39 Å20 Å2
3---2.33 Å2
Refinement stepCycle: final / Resolution: 2.2→18.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 72 206 3716
Biso mean--46.35 38.43 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133598
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173334
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.6374878
X-RAY DIFFRACTIONr_angle_other_deg2.3461.5787782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76924.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.54615626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.274154
X-RAY DIFFRACTIONr_chiral_restr0.0790.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023928
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02708
X-RAY DIFFRACTIONr_mcbond_it2.633.7051742
X-RAY DIFFRACTIONr_mcbond_other2.6113.7031741
X-RAY DIFFRACTIONr_mcangle_it3.9175.5522174
LS refinement shellResolution: 2.2→2.254 Å
RfactorNum. reflection% reflection
Rfree0.329 84 -
Rwork0.283 1539 -
obs--93.65 %

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