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- PDB-3kns: Bacillus cereus metallo-beta-lactamase Cys221Asp mutant, 20 mM Zn(II) -

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Basic information

Entry
Database: PDB / ID: 3kns
TitleBacillus cereus metallo-beta-lactamase Cys221Asp mutant, 20 mM Zn(II)
ComponentsBeta-lactamase 2
KeywordsHYDROLASE / Metallo-beta-lactamase / Zn-dependent hydrolase / Antibiotic resistance / Metal-binding
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
ACETIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsMedrano Martin, F.J. / Gonzalez, J.M. / Vila, A.J.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Metallo-beta-lactamases withstand low Zn(II) conditions by tuning metal-ligand interactions.
Authors: Gonzalez, J.M. / Meini, M.R. / Tomatis, P.E. / Medrano Martin, F.J. / Cricco, J.A. / Vila, A.J.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Sep 5, 2012Group: Database references
Revision 1.4Jun 19, 2013Group: Database references
Revision 1.5Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.6Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase 2
B: Beta-lactamase 2
C: Beta-lactamase 2
D: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,76227
Polymers100,0304
Non-polymers1,73223
Water23,7441318
1
A: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,85511
Polymers25,0071
Non-polymers84710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3546
Polymers25,0071
Non-polymers3475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1984
Polymers25,0071
Non-polymers1913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3546
Polymers25,0071
Non-polymers3475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.784, 94.341, 79.776
Angle α, β, γ (deg.)90.00, 119.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 25007.479 Da / Num. of mol.: 4 / Mutation: C168D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: 569/H/9 / Gene: blm / Plasmid: pLys S' pET-term / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04190, beta-lactamase

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Non-polymers , 5 types, 1341 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1318 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE ASP168 IN THIS ENTRY IS NAMED ASP221 ACCORDING TO THE STANDARD NUMBERING SCHEME. SEE: ...RESIDUE ASP168 IN THIS ENTRY IS NAMED ASP221 ACCORDING TO THE STANDARD NUMBERING SCHEME. SEE: GALLENI ET AL., (2001) "STANDARD NUMBERING SCHEME FOR CLASS B BETA-LACTAMASES", ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, VOL. 45, 660-663.

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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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 0.1 M Sodium Acetate, 2.8 M Ammonium Sulfate, 20 mM Zinc Sulfate, pH 4.9, Vapor diffusion, hanging drop., temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.421 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.421 Å / Relative weight: 1
ReflectionResolution: 1.58→69.34 Å / Num. obs: 132288 / % possible obs: 94.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.58-1.643.60.299188.9
1.64-1.73.90.207191.7
1.7-1.783.90.139192.4
1.78-1.873.90.099193.3
1.87-1.993.90.074194.2
1.99-2.143.90.059194.8
2.14-2.363.90.049195.8
2.36-2.73.90.043196.8
2.7-3.43.90.033197.9
3.4-503.80.024198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→23.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.15 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19364 6660 5 %RANDOM
Rwork0.16144 ---
obs0.16305 125621 94.47 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 13.475 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.43 Å2
2---0.02 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.58→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6457 0 80 1318 7855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226712
X-RAY DIFFRACTIONr_bond_other_d0.0010.024362
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9689098
X-RAY DIFFRACTIONr_angle_other_deg2.006310824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5495847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06425.884277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.263151214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5681518
X-RAY DIFFRACTIONr_chiral_restr0.1080.21067
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021183
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0821.54183
X-RAY DIFFRACTIONr_mcbond_other0.3061.51735
X-RAY DIFFRACTIONr_mcangle_it1.87826756
X-RAY DIFFRACTIONr_scbond_it2.83232529
X-RAY DIFFRACTIONr_scangle_it4.5544.52338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.581→1.622 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 437 -
Rwork0.281 8569 -
obs--87.45 %

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