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- PDB-3i15: Cobalt-substituted metallo-beta-lactamase from Bacillus cereus: r... -

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Basic information

Entry
Database: PDB / ID: 3i15
TitleCobalt-substituted metallo-beta-lactamase from Bacillus cereus: residue Cys168 fully oxidized
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 / 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 / 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: 1.55 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: Version format compliance

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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)25,1022
Polymers25,0441
Non-polymers591
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.188, 61.822, 69.521
Angle α, β, γ (deg.)90.000, 93.240, 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: 25043.531 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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
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, 40 mM CoSO4, 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: Oct 15, 2007 / 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: 1.549→40.291 Å / Num. obs: 30132 / % possible obs: 91.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 9.129
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.54-1.633.20.3632.11186737640.36377.8
1.63-1.723.20.2433.11303140550.24389.9
1.72-1.843.20.1445.21256539070.14490.9
1.84-1.993.20.089.31166936310.0892.1
1.99-2.183.20.05113.81096534190.05193.6
2.18-2.443.20.0416.51009431550.0494.9
2.44-2.824.20.0639.41170028190.06395.9
2.82-3.455.20.05112.51245224140.05197.1
3.45-4.884.60.03619.3871118920.03698.2
4.88-40.34.10.03912.6436910760.03999

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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: 1.55→40.29 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.903 / SU B: 2.883 / SU ML: 0.047 / SU R Cruickshank DPI: 0.075 / SU Rfree: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1524 5.1 %RANDOM
Rwork0.151 ---
obs0.153 30132 92.21 %-
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: 62.59 Å2 / Biso mean: 18.112 Å2 / Biso min: 2.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.58 Å2
2--1.32 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 1 266 1914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221745
X-RAY DIFFRACTIONr_bond_other_d0.0020.021131
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9582380
X-RAY DIFFRACTIONr_angle_other_deg1.61932819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20825.94674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16215318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.153155
X-RAY DIFFRACTIONr_chiral_restr0.1280.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021933
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02308
X-RAY DIFFRACTIONr_mcbond_it1.0961.51098
X-RAY DIFFRACTIONr_mcbond_other0.3161.5454
X-RAY DIFFRACTIONr_mcangle_it1.88321780
X-RAY DIFFRACTIONr_scbond_it2.8683647
X-RAY DIFFRACTIONr_scangle_it4.5774.5594
X-RAY DIFFRACTIONr_sphericity_free11.23431
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 104 -
Rwork0.293 1848 -
all-1952 -
obs--82.22 %
Refinement TLS params.Method: refined / Origin x: 8.4727 Å / Origin y: -0.8815 Å / Origin z: 18.2199 Å
111213212223313233
T0.0239 Å2-0.0013 Å20.0127 Å2-0.0272 Å2-0.0007 Å2--0.0506 Å2
L0.9729 °2-0.2436 °20.8672 °2-0.4914 °2-0.1338 °2--2.923 °2
S-0.0385 Å °0.1091 Å °0.0062 Å °-0.0299 Å °-0.0436 Å °-0.023 Å °-0.0324 Å °0.2568 Å °0.0821 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 11
2X-RAY DIFFRACTION1A15 - 31
3X-RAY DIFFRACTION1A39 - 227

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