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- PDB-6lbl: Crystal structure of IMP-1 metallo-beta-lactamase in complex with... -

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Basic information

Entry
Database: PDB / ID: 6lbl
TitleCrystal structure of IMP-1 metallo-beta-lactamase in complex with NO9 inhibitor
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
2,5-dimethyl-4-sulfamoyl-furan-3-carboxylic acid / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsWachino, J.
CitationJournal: Mbio / Year: 2020
Title: Sulfamoyl Heteroarylcarboxylic Acids as Promising Metallo-beta-Lactamase Inhibitors for Controlling Bacterial Carbapenem Resistance.
Authors: Wachino, J.I. / Jin, W. / Kimura, K. / Kurosaki, H. / Sato, A. / Arakawa, Y.
History
DepositionNov 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)25,5205
Polymers25,1471
Non-polymers3734
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.920, 56.610, 100.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NO9 / 2,5-dimethyl-4-sulfamoyl-furan-3-carboxylic acid


Mass: 219.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.03 Å3/Da / Density % sol: 39.53 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.68→56.61 Å / Num. obs: 24088 / % possible obs: 99.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.9
Reflection shellResolution: 1.68→1.77 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.281 / Num. unique obs: 3462 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ev6

5ev6


Resolution: 1.68→49.386 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.973 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.208 1187 4.938 %
Rwork0.1577 --
all0.16 --
obs-24038 99.59 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.257 Å20 Å20 Å2
2--1.241 Å20 Å2
3----0.984 Å2
Refinement stepCycle: LAST / Resolution: 1.68→49.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 17 225 1970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131812
X-RAY DIFFRACTIONr_bond_other_d00.0171698
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.652462
X-RAY DIFFRACTIONr_angle_other_deg1.3381.5853962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7395226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42824.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92915312
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg6.705151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.678153
X-RAY DIFFRACTIONr_chiral_restr0.0790.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021976
X-RAY DIFFRACTIONr_gen_planes_other00.02346
X-RAY DIFFRACTIONr_nbd_refined0.220.2349
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.21576
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2871
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2156
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1110.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0440.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.214
X-RAY DIFFRACTIONr_nbd_other0.2270.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2550.221
X-RAY DIFFRACTIONr_mcbond_it2.6392.367889
X-RAY DIFFRACTIONr_mcbond_other2.6322.363888
X-RAY DIFFRACTIONr_mcangle_it3.5693.5451111
X-RAY DIFFRACTIONr_mcangle_other3.5683.551112
X-RAY DIFFRACTIONr_scbond_it4.2592.825923
X-RAY DIFFRACTIONr_scbond_other4.2592.825924
X-RAY DIFFRACTIONr_scangle_it6.0544.0371348
X-RAY DIFFRACTIONr_scangle_other6.0514.0371349
X-RAY DIFFRACTIONr_lrange_it7.26529.6422097
X-RAY DIFFRACTIONr_lrange_other7.26829.6472098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.7240.194830.1871679X-RAY DIFFRACTION99.8866
1.724-1.7710.224920.1721604X-RAY DIFFRACTION99.9411
1.771-1.8220.244870.1711560X-RAY DIFFRACTION99.9393
1.822-1.8780.228860.1721529X-RAY DIFFRACTION100
1.878-1.940.219780.1741487X-RAY DIFFRACTION100
1.94-2.0080.245760.1691450X-RAY DIFFRACTION99.9345
2.008-2.0830.264700.1771398X-RAY DIFFRACTION100
2.083-2.1680.229690.1561349X-RAY DIFFRACTION100
2.168-2.2640.23670.1621290X-RAY DIFFRACTION99.7794
2.264-2.3750.179600.1451245X-RAY DIFFRACTION99.6944
2.375-2.5030.222550.1511174X-RAY DIFFRACTION99.5948
2.503-2.6540.187490.1571123X-RAY DIFFRACTION99.2379
2.654-2.8370.244650.1541043X-RAY DIFFRACTION98.5765
2.837-3.0630.25480.161985X-RAY DIFFRACTION99.2315
3.063-3.3550.193410.16917X-RAY DIFFRACTION98.2564
3.355-3.7480.19430.151815X-RAY DIFFRACTION98.1693
3.748-4.3240.191410.132734X-RAY DIFFRACTION98.852
4.324-5.2860.15380.143642X-RAY DIFFRACTION100
5.286-7.4350.195260.163514X-RAY DIFFRACTION100
7.435-49.3860.148130.165313X-RAY DIFFRACTION97.8979

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