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- PDB-2qz6: First crystal structure of a psychrophile class C beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 2qz6
TitleFirst crystal structure of a psychrophile class C beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / class C beta-lactamase / psychrophile / cold adaptation / Antibiotic resistance / Periplasm
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / molecular replacement / Resolution: 2.26 Å
AuthorsMichaux, C. / Massant, J. / Kerff, F. / Charlier, P. / Wouters, J.
CitationJournal: Febs J. / Year: 2008
Title: Crystal structure of a cold-adapted class C beta-lactamase
Authors: Michaux, C. / Massant, J. / Kerff, F. / Docquier, J.D. / Vandenberghe, I. / Samyn, B. / Pierrard, A. / Feller, G. / Charlier, P. / Van Beeumen, J. / Wouters, J.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)38,7651
Polymers38,7651
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.600, 69.700, 53.900
Angle α, β, γ (deg.)90.000, 90.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 38764.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas fluorescens (bacteria) / Strain: TAE 4 / References: UniProt: P85302, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 20% PEG 6K, 0.1M Tris, pH8.0, vapor diffusion, temperature 298K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 15724 / % possible obs: 95.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.94
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 16.62 / Num. unique all: 7667 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 2BLT

2blt
PDB Unreleased entry


Resolution: 2.26→19.12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.873 / Num. parameters: 10919 / Num. restraintsaints: 11088 / SU B: 5.706 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.432 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24292 722 5 %RANDOM
Rwork0.18958 ---
obs0.19224 13722 95.06 %-
all-13703 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.568 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2715
Refinement stepCycle: LAST / Resolution: 2.26→19.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 0 134 2795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222713
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9693693
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3095345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85325.189106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.69715432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.201155
X-RAY DIFFRACTIONr_chiral_restr0.0970.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022055
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21382
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21843
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7551.51772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25522783
X-RAY DIFFRACTIONr_scbond_it1.98731073
X-RAY DIFFRACTIONr_scangle_it2.9424.5910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 60 -
Rwork0.191 1048 -
obs--100 %

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