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- PDB-5tfq: Crystal structure of a representative of class A beta-lactamase f... -

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Basic information

Entry
Database: PDB / ID: 5tfq
TitleCrystal structure of a representative of class A beta-lactamase from Bacteroides cellulosilyticus DSM 14838
ComponentsBeta-lactamase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesBacteroides cellulosilyticus DSM 14838 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.07 Å
AuthorsNocek, B. / Hatzos-Skintges, C. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of a representative of class A beta-lactamase from Bacteroides cellulosilyticus DSM 14838
Authors: Nocek, B. / Hatzos-Skintges, C. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4515
Polymers31,0761
Non-polymers3744
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-14 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.837, 62.808, 87.058
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 31076.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides cellulosilyticus DSM 14838 (bacteria)
Gene: BACCELL_03967 / Production host: Escherichia coli (E. coli) / References: UniProt: E2NI36, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.4 M NaH2PO4/1.6 M K2HPO4 0.1 M Imidazole:HCl pH 8.0 0.2 M Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2016
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.07→40 Å / Num. obs: 133512 / % possible obs: 98.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.062 / Net I/av σ(I): 30.75 / Net I/σ(I): 35

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.07→40 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.639 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.024 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.134 5739 5 %RANDOM
Rwork0.11479 ---
obs0.11573 109930 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.478 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.07→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 22 411 2566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192306
X-RAY DIFFRACTIONr_bond_other_d0.0010.022219
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9833151
X-RAY DIFFRACTIONr_angle_other_deg1.29335159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.9075.373322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86226.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09215402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.218154
X-RAY DIFFRACTIONr_chiral_restr0.1280.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022712
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02484
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6991.5811154
X-RAY DIFFRACTIONr_mcbond_other1.621.5781153
X-RAY DIFFRACTIONr_mcangle_it1.9962.3811453
X-RAY DIFFRACTIONr_mcangle_other2.0212.3831454
X-RAY DIFFRACTIONr_scbond_it3.6741.9071152
X-RAY DIFFRACTIONr_scbond_other3.6721.9071152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7452.7441683
X-RAY DIFFRACTIONr_long_range_B_refined4.67116.0323080
X-RAY DIFFRACTIONr_long_range_B_other3.71114.2962805
X-RAY DIFFRACTIONr_rigid_bond_restr6.18834525
X-RAY DIFFRACTIONr_sphericity_free38.226575
X-RAY DIFFRACTIONr_sphericity_bonded10.75854813
LS refinement shellResolution: 1.071→1.099 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 129 -
Rwork0.22 2433 -
obs--25.92 %

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