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- PDB-5jmx: Crystal Structure of BcII metallo-beta-lactamase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5jmx
TitleCrystal Structure of BcII metallo-beta-lactamase in complex with DZ-305
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 / 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 / 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-DZ5 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsStepanovs, D. / McDonough, M.A. / Schofield, C.J. / Zhang, D. / Brem, J.
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
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,6978
Polymers24,9961
Non-polymers7017
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-22 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.250, 61.240, 69.050
Angle α, β, γ (deg.)90.000, 93.090, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

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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: 24995.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: blm / Production host: Escherichia coli (E. coli) / References: UniProt: P04190, beta-lactamase

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Non-polymers , 5 types, 204 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-DZ5 / (2Z)-3-(4-fluorophenyl)-2-sulfanylprop-2-enoic acid


Mass: 198.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7FO2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1MM TCEP, 5MM DZ-305, 50MM HEPES PH7.5, 100MM NACL, 0.1MM ZNCL2, 0.1M MAGNESIUM FORMATE, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2016 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.44→68.95 Å / Num. obs: 40059 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.718 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.1
Reflection shellResolution: 1.44→1.48 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.567 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
xia2data reduction
Cootmodel building
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TYT

4tyt


Resolution: 1.44→68.95 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 20.57
RfactorNum. reflection% reflection
Rfree0.1858 2008 5.01 %
Rwork0.146 --
obs0.1478 40041 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.2 Å2 / Biso mean: 29.6466 Å2 / Biso min: 11.84 Å2
Refinement stepCycle: final / Resolution: 1.44→68.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 38 198 1887
Biso mean--46.71 43.18 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011769
X-RAY DIFFRACTIONf_angle_d1.1042409
X-RAY DIFFRACTIONf_chiral_restr0.086285
X-RAY DIFFRACTIONf_plane_restr0.007304
X-RAY DIFFRACTIONf_dihedral_angle_d13.753647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.44-1.4760.34911620.334526642826100
1.476-1.51590.32241450.292827222867100
1.5159-1.56060.30531670.27226882855100
1.5606-1.61090.26961580.234426812839100
1.6109-1.66850.23321460.216826972843100
1.6685-1.73530.22881300.192927112841100
1.7353-1.81430.18321390.168527192858100
1.8143-1.910.19791430.151727202863100
1.91-2.02960.18741530.128527232876100
2.0296-2.18640.1421280.119327062834100
2.1864-2.40640.16111270.118727492876100
2.4064-2.75460.16671430.124227172860100
2.7546-3.47050.17411240.13227572881100
3.4705-69.02870.16811430.13272779292299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7141-0.84580.3814.81350.00484.1106-0.0120.39590.3663-0.1625-0.1179-0.4029-0.46320.94610.05210.2339-0.0684-0.01750.41160.080.182266.5463-0.11399.5646
25.2742-2.4755-3.56144.05126.25979.8637-0.05050.18310.2386-0.1791-0.06090.0176-0.73650.48990.06350.3182-0.0333-0.03960.28280.0470.172960.90214.30534.0608
30.2891-0.45190.91281.7858-0.34716.3228-0.09470.04770.08610.0674-0.0237-0.0359-0.22540.40240.10660.1631-0.0175-0.02590.19230.00570.153757.0586-1.549212.9647
43.358-1.31911.50365.8624-5.34276.3458-0.08850.30220.1072-0.15630.02430.0053-0.1725-0.48930.02790.19660.0025-0.02870.218-0.03560.147450.0786-0.934510.7812
56.3007-3.71930.77634.6283-0.2679.4812-0.1138-0.060.06280.085-0.00310.3299-0.5287-0.74680.10610.14040.002-0.00250.2128-0.02180.14447.9232-3.126522.2579
62.34070.00320.71345.07373.95289.18990.05090.18-0.2657-0.0426-0.07730.17850.54440.06650.09230.15480.0112-0.01790.1192-0.01150.1458.3973-11.722220.8718
72.7376-0.48710.7211.97520.82355.1071-0.01840.09020.15730.1382-0.0048-0.1561-0.02130.3943-0.0020.14110.011-0.03040.16040.02690.149566.7047-4.999325.7317
83.5301-0.1731-0.36642.90990.05144.5494-0.09490.0466-0.19050.04970.0313-0.12020.4340.63340.06410.15480.0508-0.03780.2136-0.00070.151568.615-10.369426.8833
97.4675-2.66-5.58636.97441.28174.9224-0.079-0.2848-0.02340.2930.0299-0.11340.15460.4191-0.00990.17690.0267-0.08830.3068-0.0060.183773.5134-6.071132.0007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 90 )A37 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 105 )A91 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 124 )A106 - 124
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 138 )A125 - 138
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 159 )A139 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 184 )A160 - 184
7X-RAY DIFFRACTION7chain 'A' and (resid 185 through 217 )A185 - 217
8X-RAY DIFFRACTION8chain 'A' and (resid 218 through 245 )A218 - 245
9X-RAY DIFFRACTION9chain 'A' and (resid 246 through 257 )A246 - 257

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