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- PDB-8btu: Structure of D179N BlaC from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8btu
TitleStructure of D179N BlaC from Mycobacterium tuberculosis
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region
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/transpeptidase-like
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChikunova, A. / Bruenle, S. / Ubbink, M.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)ECHO-711.016.002 Netherlands
CitationJournal: Febs J. / Year: 2023
Title: Asp179 in the class A beta-lactamase from Mycobacterium tuberculosis is a conserved yet not essential residue due to epistasis.
Authors: van Alen, I. / Chikunova, A. / van Zanten, D.B. / de Block, A.A. / Timmer, M. / Brunle, S. / Ubbink, M.
History
DepositionNov 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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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)28,3291
Polymers28,3291
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10840 Å2
Unit cell
Length a, b, c (Å)38.370, 54.050, 53.640
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / Ambler class A beta-lactamase


Mass: 28328.789 Da / Num. of mol.: 1 / Mutation: D179N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: blaC, blaA, MT2128 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WKD2, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M ammonium acetate; 0.1 M BIS-TRIS buffer; 17% w/v PEG 10K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→38.34 Å / Num. obs: 20045 / % possible obs: 98.4 % / Redundancy: 1.8 % / CC1/2: 0.988 / Rpim(I) all: 0.091 / Net I/σ(I): 5.2
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1404 / CC1/2: 0.591 / Rpim(I) all: 0.427 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 1.8→38.34 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.69 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 1043 5.2 %RANDOM
Rwork0.18051 ---
obs0.18356 19002 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å2-0 Å20.56 Å2
2--0.43 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 0 207 2199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122040
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161854
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6522786
X-RAY DIFFRACTIONr_angle_other_deg0.4381.564304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0155267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.402519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84810305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0590.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
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_it1.3231.9251068
X-RAY DIFFRACTIONr_mcbond_other1.3181.9251068
X-RAY DIFFRACTIONr_mcangle_it2.0732.8781335
X-RAY DIFFRACTIONr_mcangle_other2.0732.8791336
X-RAY DIFFRACTIONr_scbond_it1.7312.088972
X-RAY DIFFRACTIONr_scbond_other1.732.088973
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5953.071452
X-RAY DIFFRACTIONr_long_range_B_refined4.39432.2952370
X-RAY DIFFRACTIONr_long_range_B_other4.17730.2282315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 69 -
Rwork0.379 1404 -
obs--97.04 %

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