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- PDB-5w8w: Bacillus cereus Zn-dependent metallo-beta-lactamase at pH 7 - new... -

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Basic information

Entry
Database: PDB / ID: 5w8w
TitleBacillus cereus Zn-dependent metallo-beta-lactamase at pH 7 - new refinement
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE
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
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGonzalez, J.M. / Shabalin, I.G. / Raczynska, J.E. / Jaskolski, M. / Minor, W. / Wlodawer, A. / Gonzalez, M.M. / Vila, A.J.
CitationJournal: Drug Resist. Updat. / Year: 2018
Title: A close look onto structural models and primary ligands of metallo-beta-lactamases.
Authors: Raczynska, J.E. / Shabalin, I.G. / Minor, W. / Wlodawer, A. / Jaskolski, M.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionJul 12, 2017ID: 4NQ7
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)24,6505
Polymers24,4231
Non-polymers2274
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-85 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.603, 60.419, 69.513
Angle α, β, γ (deg.)90.000, 93.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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: 24422.902 Da / Num. of mol.: 1 / Fragment: residues 36-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: blm / Plasmid: PET27B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04190, 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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 180mM K2SO4, protein at 15mg/ml in 10mM Tris-HCl pH7, 50mM NaCl, 1mM DTT, 1mM Zn2SO4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→35.4 Å / Num. obs: 9273 / % possible obs: 87.4 %
Reflection shellResolution: 2.25→2.308 Å / Num. unique obs: 60 / % possible all: 80.11

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0158refinement
PHASERphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NQ4

4nq4


Resolution: 2.25→35.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.864 / SU ML: 0.158 / SU R Cruickshank DPI: 0.4503 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.246
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 915 9.9 %RANDOM
Rwork0.1525 ---
obs0.1588 8356 87.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.73 Å2 / Biso mean: 38.215 Å2 / Biso min: 19.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-0.3 Å2
2--3.36 Å20 Å2
3----2.7 Å2
Refinement stepCycle: final / Resolution: 2.25→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 8 107 1783
Biso mean--55.09 42.01 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191706
X-RAY DIFFRACTIONr_bond_other_d0.0020.021624
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9652312
X-RAY DIFFRACTIONr_angle_other_deg0.9493.0013763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3965216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28725.60666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70715304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.55155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021857
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02304
X-RAY DIFFRACTIONr_sphericity_bonded22.64652
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 67 -
Rwork0.199 533 -
all-600 -
obs--80.11 %
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)
112.1373-6.2254-2.481511.1417-1.64739.8444-0.00330.37290.5339-0.3637-0.1384-0.7648-0.39940.20120.14180.2253-0.15620.01440.31870.02360.167317.62410.1786.277
24.08911.84141.20243.94360.88876.57010.05230.0134-0.11080.0279-0.1184-0.148-0.19080.50640.0660.0428-0.03730.00320.23780.03750.085513.7181.94710.482
31.5071-0.29810.00071.0039-0.56686.0075-0.02230.05720.0385-0.0108-0.0080.0451-0.2406-0.0190.03040.0241-0.0174-0.01940.0567-0.01070.05911.6541.73512.98
42.2687-0.4082-0.22881.56580.6554.7062-0.0261-0.14440.03570.09630.0734-0.13510.20430.5894-0.04740.020.048-0.01190.1538-0.00220.039212.649-4.29225.563
57.2848-0.8681-2.368711.02357.583416.71560.0113-0.3291-0.12680.21760.0928-0.00740.3140.5389-0.10420.03120.034-0.05710.32040.00730.144520.396-1.78932.407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 48
2X-RAY DIFFRACTION2A49 - 81
3X-RAY DIFFRACTION3A82 - 167
4X-RAY DIFFRACTION4A168 - 245
5X-RAY DIFFRACTION5A246 - 257

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