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- PDB-2nze: Structure of beta-lactamase II from Bacillus cereus. R121H, C221S... -

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Basic information

Entry
Database: PDB / ID: 2nze
TitleStructure of beta-lactamase II from Bacillus cereus. R121H, C221S double mutant. Space group P3121.
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
ACETIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase II
B: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,23921
Polymers48,7762
Non-polymers1,46419
Water6,575365
1
A: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,16611
Polymers24,3881
Non-polymers77810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,07410
Polymers24,3881
Non-polymers6869
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Beta-lactamase II
hetero molecules

B: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,14720
Polymers48,7762
Non-polymers1,37218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area3600 Å2
ΔGint-177 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.665, 66.665, 175.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-834-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 24387.791 Da / Num. of mol.: 2 / Mutation: yes
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

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Non-polymers , 5 types, 384 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 0.1 M sodium acetate, 2.8 M ammonium sulfate, pH 4.9, 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 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 40696 / % possible obs: 94.8 % / Observed criterion σ(I): 202606 / Redundancy: 5.2 % / Rsym value: 0.061 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.45 / % possible all: 91.9

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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: 1.8→58.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.457 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2060 5.1 %RANDOM
Rwork0.175 ---
obs0.177 40696 94.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.194 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→58.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 82 365 3793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223469
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9754689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06125.839137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06615629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.435158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022488
X-RAY DIFFRACTIONr_nbd_refined0.2010.21959
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22343
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2442
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.225
X-RAY DIFFRACTIONr_mcbond_it0.9481.52185
X-RAY DIFFRACTIONr_mcangle_it1.57723466
X-RAY DIFFRACTIONr_scbond_it2.36331412
X-RAY DIFFRACTIONr_scangle_it3.7764.51223
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 143 -
Rwork0.249 2718 -
obs-2861 91.93 %

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