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- PDB-6k4x: Crystal structure of SMB-1 metallo-beta-lactamase in a complex wi... -

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Basic information

Entry
Database: PDB / ID: 6k4x
TitleCrystal structure of SMB-1 metallo-beta-lactamase in a complex with ASB
ComponentsMetallo-beta-lactamase
KeywordsHYDROLASE / metallo-beta-lactamase
Function / homology
Function and homology information


: / Metallo-beta-lactamase superfamily / 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
4-azanyl-2-sulfanyl-benzoic acid / Metallo-beta-lactamase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 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
DepositionMay 27, 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 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4648
Polymers27,7541
Non-polymers7107
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.997, 41.682, 45.660
Angle α, β, γ (deg.)108.75, 102.79, 105.86
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metallo-beta-lactamase / Metallo-beta-lactamase type 2


Mass: 27754.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: SMB-1 / Production host: Escherichia coli (E. coli) / References: UniProt: G5ELM3, beta-lactamase

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Non-polymers , 5 types, 544 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-D0U / 4-azanyl-2-sulfanyl-benzoic acid


Mass: 169.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulfate, 0.1M Tris-HCl (pH 8.5), 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. obs: 73794 / % possible obs: 93.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 37.3
Reflection shellResolution: 1.17→1.19 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.087 / Num. unique obs: 2884 / % possible all: 71.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B1U

5b1u


Resolution: 1.17→33.5 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.401 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15053 3714 5 %RANDOM
Rwork0.12941 ---
obs0.13049 70078 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.61 Å2-0.32 Å2
2--0.82 Å2-0.56 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.17→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 36 537 2505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0142108
X-RAY DIFFRACTIONr_bond_other_d00.0171866
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.6752878
X-RAY DIFFRACTIONr_angle_other_deg1.0771.6554396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0385288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26221.748103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77315346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2681515
X-RAY DIFFRACTIONr_chiral_restr0.3020.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02381
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_it0.8760.7621073
X-RAY DIFFRACTIONr_mcbond_other0.870.761071
X-RAY DIFFRACTIONr_mcangle_it1.2041.1491347
X-RAY DIFFRACTIONr_mcangle_other1.2071.151348
X-RAY DIFFRACTIONr_scbond_it1.8140.9751035
X-RAY DIFFRACTIONr_scbond_other1.7850.9631024
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6031.371500
X-RAY DIFFRACTIONr_long_range_B_refined4.05711.612505
X-RAY DIFFRACTIONr_long_range_B_other3.5059.9552322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.171→1.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.164 262 -
Rwork0.143 4679 -
obs--85.13 %

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