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- PDB-6dr8: Metallo-beta-lactamase from Cronobacter sakazakii (Enterobacter s... -

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Basic information

Entry
Database: PDB / ID: 6dr8
TitleMetallo-beta-lactamase from Cronobacter sakazakii (Enterobacter sakazakii) HARLDQ motif mutant S60/R118H/Q121H/K254H
ComponentsBeta-lactamase
KeywordsHYDROLASE / Metallo-beta-lactamse / METAL BINDING PROTEIN / Beta-lactamase
Function / homology
Function and homology information


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
(2-hydroxyethoxy)acetaldehyde / TRIETHYLENE GLYCOL / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesCronobacter sakazakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.476 Å
AuthorsMonteiro Pedroso, M. / Waite, D. / Natasa, M. / McGeary, R. / Guddat, L. / Hugenholtz, P. / Schenk, G.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP108477 Australia
Australian Research Council (ARC)DP150104358 Australia
Australian Research Council (ARC)T120100694 Australia
CitationJournal: Protein Cell / Year: 2020
Title: Broad spectrum antibiotic-degrading metallo-beta-lactamases are phylogenetically diverse
Authors: Monteiro Pedroso, M. / Waite, D. / Melse, O. / Wilson, L. / Mitic, N. / McGeary, R. / Antes, I. / Guddat, L. / Hugenholtz, P. / Schenk, G.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,53912
Polymers28,3691
Non-polymers1,16911
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.767, 69.151, 77.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 28369.172 Da / Num. of mol.: 1 / Mutation: R118H, Q121H, K254H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cronobacter sakazakii (bacteria) / Gene: CSK29544_03680 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6VWC7

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Non-polymers , 5 types, 188 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-1KA / (2-hydroxyethoxy)acetaldehyde


Mass: 104.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.49 M NaH2PO4 0.91 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.7107 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 20, 2016
RadiationMonochromator: MX2 Beamline Australian Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 1.476→43.77 Å / Num. obs: 39943 / % possible obs: 99 % / Redundancy: 6.9 % / R split: 0.0459 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.064 / Net I/σ(I): 10.1
Reflection shellResolution: 1.48→1.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 2 / Num. unique obs: 1589 / R split: 0.057 / Rpim(I) all: 0.455 / % possible all: 81

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Blu-Icedata collection
HKL-2000data reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DN4

6dn4


Resolution: 1.476→34.575 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1667 1998 5.02 %
Rwork0.1322 --
obs0.1339 39840 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.476→34.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 66 177 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072097
X-RAY DIFFRACTIONf_angle_d0.9452843
X-RAY DIFFRACTIONf_dihedral_angle_d16.016773
X-RAY DIFFRACTIONf_chiral_restr0.079298
X-RAY DIFFRACTIONf_plane_restr0.007371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.476-1.51290.25521220.2122311X-RAY DIFFRACTION85
1.5129-1.55380.24451420.17332681X-RAY DIFFRACTION100
1.5538-1.59960.19911410.15832686X-RAY DIFFRACTION100
1.5996-1.65120.20811440.13522714X-RAY DIFFRACTION100
1.6512-1.71020.16311420.12032694X-RAY DIFFRACTION100
1.7102-1.77870.14811430.11092701X-RAY DIFFRACTION100
1.7787-1.85960.15191430.09912724X-RAY DIFFRACTION100
1.8596-1.95760.1341430.09292692X-RAY DIFFRACTION100
1.9576-2.08030.12741430.09142729X-RAY DIFFRACTION100
2.0803-2.24090.11531440.09412721X-RAY DIFFRACTION100
2.2409-2.46630.15661460.10282750X-RAY DIFFRACTION100
2.4663-2.82310.17071450.12552762X-RAY DIFFRACTION100
2.8231-3.55620.15911470.14322793X-RAY DIFFRACTION100
3.5562-34.5850.18771530.17392884X-RAY DIFFRACTION99

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