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- PDB-7a74: Structure of G132N BlaC from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7a74
TitleStructure of G132N BlaC from Mycobacterium tuberculosis
ComponentsBeta-lactamase
KeywordsHYDROLASE / BlaC / beta-lactamase / Mycobacterium tuberculosis
Function / homology
Function and homology information


: / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
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
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChikunova, A. / Ahmad, M.U. / Perrakis, A. / Ubbink, M.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)ECHO-711.016.002 Netherlands
H2020 Marie Curie Actions of the European Commission653706 Netherlands
CitationJournal: Antimicrob.Agents Chemother. / Year: 2021
Title: Two beta-Lactamase Variants with Reduced Clavulanic Acid Inhibition Display Different Millisecond Dynamics.
Authors: Elings, W. / Chikunova, A. / van Zanten, D.B. / Drenth, R. / Ahmad, M.U.D. / Blok, A.J. / Timmer, M. / Perrakis, A. / Ubbink, M.
History
DepositionAug 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.pdbx_mutation / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.2Jul 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,88022
Polymers28,4901
Non-polymers1,39021
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint16 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.007, 54.596, 79.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 28489.898 Da / Num. of mol.: 1 / Mutation: G132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: blaC, blaA, Rv2068c, MTCY49.07c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WKD3, beta-lactamase

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Non-polymers , 5 types, 186 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 0.1 M Imidazole, 0.09 M Halogens (Sodium Bromide, Sodium Iodide, Sodium Fluoride), 30% w/v EDO P8K mix(Ethylene Glycol, PEG 8000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.912 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.6→45.03 Å / Num. obs: 31258 / % possible obs: 99 % / Redundancy: 1.8 % / CC1/2: 0.997 / Rpim(I) all: 0.056 / Net I/σ(I): 6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1434 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 1.6→45.03 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.67 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18785 1560 5 %RANDOM
Rwork0.1552 ---
obs0.15682 29653 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.978 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å2-0 Å2
2---0.55 Å20 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 1.6→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 87 165 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0172230
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192125
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.8753025
X-RAY DIFFRACTIONr_angle_other_deg1.2012.5834877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4120.973113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34215325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4461520
X-RAY DIFFRACTIONr_chiral_restr0.0890.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
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_it1.2041.2951134
X-RAY DIFFRACTIONr_mcbond_other1.1951.2931133
X-RAY DIFFRACTIONr_mcangle_it1.8531.9391432
X-RAY DIFFRACTIONr_mcangle_other1.8571.9411433
X-RAY DIFFRACTIONr_scbond_it2.1041.5891096
X-RAY DIFFRACTIONr_scbond_other2.1031.5911097
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0132.2411593
X-RAY DIFFRACTIONr_long_range_B_refined4.81817.0252572
X-RAY DIFFRACTIONr_long_range_B_other4.81717.0372573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 85 -
Rwork0.218 2040 -
obs--93 %

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