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- PDB-4nq4: Bacillus cereus Zn-dependent metallo-beta-lactamase at pH 7 -

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Basic information

Entry
Database: PDB / ID: 4nq4
TitleBacillus cereus Zn-dependent metallo-beta-lactamase at pH 7
ComponentsBeta-lactamase 2
KeywordsHYDROLASE / lactamase / metallo-beta-lactamase superfamily
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 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 / molecular replacement / Resolution: 1.67 Å
AuthorsGonzalez, J.M. / Gonzalez, M.M. / Vila, A.J.
CitationJournal: TO BE PUBLISHED
Title: Inhibition of metallo-lactamases with bicyclic compounds
Authors: Gonzalez, M.M. / Gonzalez, J.M. / Vila, A.J.
History
DepositionNov 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5934
Polymers24,4231
Non-polymers1703
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.115, 60.810, 69.251
Angle α, β, γ (deg.)90.000, 93.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase 2 / Beta-lactamase II / Cephalosporinase / Penicillinase


Mass: 24422.902 Da / Num. of mol.: 1 / Fragment: UNP 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
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: 1.67→40 Å / Num. obs: 22467

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→34.6 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.3603 / WRfactor Rwork: 0.2805 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7715 / SU B: 2.965 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1577 / SU Rfree: 0.1574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 1169 5.2 %RANDOM
Rwork0.243 ---
obs0.246 22467 87.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.25 Å2 / Biso mean: 23.2352 Å2 / Biso min: 6.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å2-0.71 Å2
2--0.73 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.67→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 3 151 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191725
X-RAY DIFFRACTIONr_bond_other_d0.0010.021676
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9572344
X-RAY DIFFRACTIONr_angle_other_deg0.933.0013852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.035222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33225.77571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61415301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.731155
X-RAY DIFFRACTIONr_chiral_restr0.1140.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 70 -
Rwork0.288 1386 -
all-1456 -
obs--77.74 %

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