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- PDB-6eum: CRYSTAL STRUCTURE OF BCII METALLO-BETA-LACTAMASE IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 6eum
TitleCRYSTAL STRUCTURE OF BCII METALLO-BETA-LACTAMASE IN COMPLEX WITH DZ-307
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / ANTIMICROBIAL RESISTANCE / METALLO BETA LACTAMASE / INHIBITOR
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 / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase ...: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / 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
Chem-BY5 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsStepanovs, D. / McDonough, M.A. / Schofield, C.J. / Zhang, D. / El-Husseiny, A. / Brem, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Wellcome Trust United Kingdom
CitationJournal: Bioorg. Med. Chem. / Year: 2018
Title: Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases.
Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. ...Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. / McDonough, M.A. / Schofield, C.J.
History
DepositionOct 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)25,6577
Polymers25,0121
Non-polymers6456
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-21 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.180, 61.440, 70.180
Angle α, β, γ (deg.)90.000, 93.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase II / Cephalosporinase / Metallo-beta-lactamase type II / ...B2 metallo-beta-lactamase / Beta-lactamase II / Cephalosporinase / Metallo-beta-lactamase type II / Metallothioprotein beta-lactamase II / Penicillinase / Zinc-requiring beta-lactamase II


Mass: 25011.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: blm / Plasmid: PET9a / Production host: Escherichia coli (E. coli) / References: UniProt: P04190, beta-lactamase

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Non-polymers , 5 types, 246 molecules

#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-BY5 / (~{Z})-2-sulfanyl-3-[2,3,6-tris(fluoranyl)phenyl]prop-2-enoic acid


Mass: 234.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H5F3O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 45 % / Description: rhombohedron
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1MM TCEP, 5MM DZ-307, 50MM HEPES pH7.5, 100MM NACL, 0.1MM ZNCL2, 0.1M MAGNESIUM FORMATE, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2016
RadiationMonochromator: double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.18→35.5 Å / Num. obs: 72015 / % possible obs: 97.5 % / Redundancy: 16.5 % / Biso Wilson estimate: 12.306 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.025 / Rrim(I) all: 0.101 / Net I/σ(I): 14.1
Reflection shellResolution: 1.18→1.21 Å / Redundancy: 17 % / Rmerge(I) obs: 2.489 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5168 / CC1/2: 0.563 / Rpim(I) all: 0.631 / Rrim(I) all: 2.642 / % possible all: 94.9

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TYT
Resolution: 1.18→19.529 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.96
RfactorNum. reflection% reflectionSelection details
Rfree0.1511 3416 4.75 %RANDOM SELECTION
Rwork0.1277 ---
obs0.1289 71973 97.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.68 Å2 / Biso mean: 24.4404 Å2 / Biso min: 10.8 Å2
Refinement stepCycle: LAST / Resolution: 1.18→19.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 34 240 1974
LS refinement shellResolution: 1.18→1.1969 Å
RfactorNum. reflection% reflection
Rfree0.3063 131 4.5 %
Rwork0.2978 2900 -
obs--94 %

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