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- PDB-1dxk: Metallo-beta-lactamase from Bacillus cereus 569/H/9 C168S mutant -

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Basic information

Entry
Database: PDB / ID: 1dxk
TitleMetallo-beta-lactamase from Bacillus cereus 569/H/9 C168S mutant
ComponentsCLASS B BETA-LACTAMASE
KeywordsHYDROLASE / HYDROLASE (BETA-LACTAMASE) / METALLO BETA-LACTAMASE / ZINC
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.85 Å
AuthorsChantalat, L. / Duee, E. / Dideberg, O.
Citation
Journal: Protein Sci. / Year: 2000
Title: Structural effects of the active site mutation cysteine to serine in Bacillus cereus zinc-beta-lactamase.
Authors: Chantalat, L. / Duee, E. / Galleni, M. / Frere, J.M. / Dideberg, O.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: 1.85 A Resolution Structure of the Zinc(II) Beta-Lactamase from Bacillus Cereus
Authors: Carfi, A. / Duee, E. / Galleni, M. / Frere, J.M. / Dideberg, O.
#2: Journal: Embo J. / Year: 1995
Title: The 3-D Structure of a Zinc Metallo-Beta-Lactamase from Bacillus Cereus Reveals a New Type of Protein Fold
Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.M. / Dideberg, O.
History
DepositionJan 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2Oct 24, 2018Group: Advisory / Data collection / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _entity_src_gen.gene_src_strain
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Dec 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: CLASS B BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1063
Polymers24,9791
Non-polymers1262
Water4,179232
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.790, 61.250, 69.280
Angle α, β, γ (deg.)90.00, 92.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CLASS B BETA-LACTAMASE / PENICILLINASE / CEPHALOSPORINASE


Mass: 24979.469 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: 1MM ZN IN THE BUFFER / Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Plasmid: PRTWHO12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH1 / References: UniProt: P04190, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 38 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
210 mMcacodylate sodium1drop
313 %PEG80001reservoir
410 mMsodium citrate1reservoir
50.100 mMdithiothreitol1reservoir
6100 mMMES1reservoir
71 mM1reservoirZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 17009 / % possible obs: 89.9 % / Redundancy: 3.82 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.043
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.75 % / Rsym value: 0.069 / % possible all: 88.8
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 88.8 % / Num. unique obs: 1648 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1BVT

1bvt


Resolution: 1.85→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: DISORDERED RESIDUES, (I.E. FOR WHICH NO COORDINATES ARE REPORTED BUT THE OCCUPANCY IS SET TO ZERO) ARE 11 - 14, 32 - 38, AND GLU 212 HAS TWO CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 819 4.9 %RANDOM
Rwork0.2054 ---
obs0.2054 16822 90.1 %-
Displacement parametersBiso mean: 17.57 Å2
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 5 232 1947
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.638
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3343 98 4.79 %
Rwork0.2959 1949 -
obs--87.7 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2612
Solvent computation
*PLUS
Displacement parameters
*PLUS

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