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- PDB-2nyp: Structure of beta-lactamase II from Bacillus cereus. R121H, C221D... -

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Basic information

Entry
Database: PDB / ID: 2nyp
TitleStructure of beta-lactamase II from Bacillus cereus. R121H, C221D doble mutant with two zinc ions.
ComponentsBeta-lactamase II
KeywordsHYDROLASE / Beta-lactamase II / Bacillus cereus
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 superfamily / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMedrano Martin, F.J. / Vila, A.J. / Gonzalez, J.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Zn2 position in metallo-beta-lactamases is critical for activity: a study on chimeric metal sites on a conserved protein scaffold.
Authors: Gonzalez, J.M. / Medrano Martin, F.J. / Costello, A.L. / Tierney, D.L. / Vila, A.J.
History
DepositionNov 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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

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Assembly

Deposited unit
A: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4173
Polymers24,2871
Non-polymers1312
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.464, 61.023, 68.710
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 24286.621 Da / Num. of mol.: 1 / Mutation: y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: blm / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1 M sodium cacodylate,60 mM sodium tartrate, 18% PEG 3350, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.42 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 18461 / % possible obs: 97.6 % / Observed criterion σ(I): 45536 / Redundancy: 2.6 % / Rsym value: 0.047 / Net I/σ(I): 12.4
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.277 / % possible all: 86.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bc2

1bc2


Resolution: 1.84→68.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.271 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 947 5.1 %RANDOM
Rwork0.179 ---
obs0.182 18461 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.794 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.89 Å2
2--0.52 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.84→68.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 2 234 1904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221695
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9592297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4155213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.19525.94269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0915312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.016154
X-RAY DIFFRACTIONr_chiral_restr0.1080.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021225
X-RAY DIFFRACTIONr_nbd_refined0.2090.21009
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2261
X-RAY DIFFRACTIONr_metal_ion_refined0.0130.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.217
X-RAY DIFFRACTIONr_mcbond_it0.9861.51077
X-RAY DIFFRACTIONr_mcangle_it1.58421717
X-RAY DIFFRACTIONr_scbond_it2.4213684
X-RAY DIFFRACTIONr_scangle_it3.7484.5580
LS refinement shellResolution: 1.841→1.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 53 -
Rwork0.271 1106 -
obs-1159 84.54 %

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