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- PDB-6jed: Crystal structure of IMP-1 metallo-beta-lactamase in a complex wi... -

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Basic information

Entry
Database: PDB / ID: 6jed
TitleCrystal structure of IMP-1 metallo-beta-lactamase in a complex with MCR
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / metallo-beta-lactamase
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
SULFANYLACETIC ACID / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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
DepositionFeb 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,6085
Polymers25,1471
Non-polymers4614
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-79 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.920, 56.820, 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 / IMP-1 metallo-beta-lactamase / B2 metallo-beta-lactamase / BLA-IMP / IMP-1 / Beta-lactamase type II ...IMP-1 metallo-beta-lactamase / 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-MCR / SULFANYLACETIC ACID / MERCAPTOACETIC ACID


Mass: 92.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2S
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate, 0.1M sodium HEPES buffer (pH 7.5), 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→56.82 Å / Num. obs: 29943 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.2
Reflection shellResolution: 1.57→1.65 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 4256 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y5B

5y5b


Resolution: 1.57→50.53 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.446 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19969 1514 5.1 %RANDOM
Rwork0.16477 ---
obs0.16654 28368 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.085 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.64 Å2
Refinement stepCycle: 1 / Resolution: 1.57→50.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 22 201 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0141824
X-RAY DIFFRACTIONr_bond_other_d00.0171706
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.6582481
X-RAY DIFFRACTIONr_angle_other_deg0.9411.6564005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7495230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37124.73776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38615317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.798153
X-RAY DIFFRACTIONr_chiral_restr0.2790.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021996
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
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_it2.4211.9893
X-RAY DIFFRACTIONr_mcbond_other2.411.896892
X-RAY DIFFRACTIONr_mcangle_it3.4052.8391117
X-RAY DIFFRACTIONr_mcangle_other3.4052.8441118
X-RAY DIFFRACTIONr_scbond_it3.5692.313931
X-RAY DIFFRACTIONr_scbond_other3.5682.313931
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2153.2941360
X-RAY DIFFRACTIONr_long_range_B_refined6.57823.6742070
X-RAY DIFFRACTIONr_long_range_B_other6.50523.1442028
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.566→1.607 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 117 -
Rwork0.193 2014 -
obs--99.86 %

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