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- PDB-3i13: Bacillus cereus Zn-dependent metallo-beta-lactamase at pH 5.8 -

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Basic information

Entry
Database: PDB / ID: 3i13
TitleBacillus cereus Zn-dependent metallo-beta-lactamase at pH 5.8
ComponentsBeta-lactamase 2
KeywordsHYDROLASE / Antibiotic resistance / Metallo-beta-lactamase superfamily / Zn-dependent hydrolase / 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
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsGonzalez, J.M. / Buschiazzo, A. / Vila, A.J.
CitationJournal: Biochemistry / Year: 2010
Title: Evidence of adaptability in metal coordination geometry and active-site loop conformation among B1 metallo-beta-lactamases .
Authors: Gonzalez, J.M. / Buschiazzo, A. / Vila, A.J.
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 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_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.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_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)25,1263
Polymers24,9961
Non-polymers1312
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.111, 61.410, 69.483
Angle α, β, γ (deg.)90.000, 93.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 24995.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: 569/H/9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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.: 220 / 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: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1 M Sodium cacodylate, 0.1 M Sodium tartrate, 18% PEG 3350, 1 mM ZnSO4, 1 mM DTT, pH 5.8, Vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2008 / Details: mirrors
RadiationMonochromator: multilayer mirrors (Varimax-HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→20.546 Å / Num. obs: 21061 / % possible obs: 92 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 11.56
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.1 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.74-1.830.4011.9631929970.40190.1
1.83-1.950.252.9613028830.2590.9
1.95-2.080.1534.8566526810.15391.7
2.08-2.250.0997.2544625680.09992.5
2.25-2.460.06910.2502023700.06993.8
2.46-2.750.05213.7462721820.05294.5
2.75-3.180.04215.3411019540.04295.7
3.18-3.890.03121344516320.03195.1
3.89-5.50.02723247912010.02790.1
5.5-20.550.02426.412255930.02478.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→20.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.154 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.874 / SU B: 5.177 / SU ML: 0.077 / SU R Cruickshank DPI: 0.112 / SU Rfree: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1045 5 %RANDOM
Rwork0.159 ---
obs0.161 21059 91.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 53.5 Å2 / Biso mean: 23.989 Å2 / Biso min: 9.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å2-0.38 Å2
2--1.6 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.74→20.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 2 220 1850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221689
X-RAY DIFFRACTIONr_bond_other_d0.0010.021094
X-RAY DIFFRACTIONr_angle_refined_deg1.761.962299
X-RAY DIFFRACTIONr_angle_other_deg1.0432710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.63825.73568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20415298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.171155
X-RAY DIFFRACTIONr_chiral_restr0.110.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
X-RAY DIFFRACTIONr_mcbond_it0.9871.51075
X-RAY DIFFRACTIONr_mcbond_other0.3521.5449
X-RAY DIFFRACTIONr_mcangle_it1.60821734
X-RAY DIFFRACTIONr_scbond_it2.7143614
X-RAY DIFFRACTIONr_scangle_it4.3274.5561
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 69 -
Rwork0.252 1436 -
all-1505 -
obs--89.48 %
Refinement TLS params.Method: refined / Origin x: 8.6958 Å / Origin y: -0.6071 Å / Origin z: 18.2487 Å
111213212223313233
T0.0189 Å2-0.0101 Å20.0158 Å2-0.0273 Å20.0005 Å2--0.0565 Å2
L1.1027 °2-0.4674 °21.0258 °2-0.7387 °2-0.1487 °2--3.0859 °2
S-0.0606 Å °0.1265 Å °0.0358 Å °0.0057 Å °-0.0471 Å °-0.0556 Å °-0.0471 Å °0.2654 Å °0.1076 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 31
2X-RAY DIFFRACTION1A39 - 227

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