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- PDB-5y5b: Crystal Structure Of IMP-1 Metallo-beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 5y5b
TitleCrystal Structure Of IMP-1 Metallo-beta-lactamase
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...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 / 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
Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWachino, J.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: 4-Amino-2-Sulfanylbenzoic Acid as a Potent Subclass B3 Metallo-beta-Lactamase-Specific Inhibitor Applicable for Distinguishing Metallo-beta-Lactamase Subclasses.
Authors: Wachino, J. / Kanechi, R. / Nishino, E. / Mochizuki, M. / Jin, W. / Kimura, K. / Kurosaki, H. / Arakawa, Y.
History
DepositionAug 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 19, 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,8506
Polymers25,1471
Non-polymers7035
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-65 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.010, 57.730, 101.060
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 / BLA-IMP / IMP-1 / Beta-lactamase type II / Metallo-beta-lactamase type II


Mass: 25146.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P52699, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 3350, 0.2M sodium acetate, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.7→57.73 Å / Num. obs: 23964 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 23.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.314 / Num. unique all: 3420 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ev6

5ev6


Resolution: 1.7→50.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.743 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19876 1180 4.9 %RANDOM
Rwork0.15454 ---
obs0.15674 22727 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.615 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--1.09 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 37 250 2015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021831
X-RAY DIFFRACTIONr_bond_other_d0.0010.021728
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.9882488
X-RAY DIFFRACTIONr_angle_other_deg0.62734037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9655226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44725.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06615312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.288153
X-RAY DIFFRACTIONr_chiral_restr0.3910.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211960
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02343
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_it1.6521.324889
X-RAY DIFFRACTIONr_mcbond_other1.6411.322888
X-RAY DIFFRACTIONr_mcangle_it2.4231.9781111
X-RAY DIFFRACTIONr_mcangle_other2.4261.9821112
X-RAY DIFFRACTIONr_scbond_it2.9611.731942
X-RAY DIFFRACTIONr_scbond_other2.961.731943
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.382.4391375
X-RAY DIFFRACTIONr_long_range_B_refined5.80317.6382101
X-RAY DIFFRACTIONr_long_range_B_other5.62916.9132038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 89 -
Rwork0.172 1647 -
obs--100 %

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