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- PDB-7a5u: Structure of E37A BlaC from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7a5u
TitleStructure of E37A 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 / 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/transpeptidase-like
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Febs J. / Year: 2021
Title: Conserved residues Glu37 and Trp229 play an essential role in protein folding of beta-lactamase.
Authors: Chikunova, A. / Manley, M.P. / Ud Din Ahmad, M. / Bilman, T. / Perrakis, A. / Ubbink, M.
History
DepositionAug 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,4651
Polymers29,4651
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11090 Å2
Unit cell
Length a, b, c (Å)38.560, 54.739, 54.509
Angle α, β, γ (deg.)90.00, 95.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 29465.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A655AHQ9, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate, 0.2 M magnesium chloride, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.5→54.3 Å / Num. obs: 33194 / % possible obs: 91.5 % / Redundancy: 2.5 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 10.2
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1765 / CC1/2: 0.768 / Rpim(I) all: 0.358 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 1.5→54.36 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.487 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17622 1688 5.1 %RANDOM
Rwork0.12456 ---
obs0.12703 31487 91.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.396 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å2-0 Å2-0.35 Å2
2---1.91 Å2-0 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.5→54.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 0 146 2150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132070
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171935
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.6522827
X-RAY DIFFRACTIONr_angle_other_deg1.6031.5794462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33720.811111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34315312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8151520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
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_it1.9361.3841075
X-RAY DIFFRACTIONr_mcbond_other1.9271.3821074
X-RAY DIFFRACTIONr_mcangle_it2.3362.0821339
X-RAY DIFFRACTIONr_mcangle_other2.342.0841340
X-RAY DIFFRACTIONr_scbond_it2.711.719995
X-RAY DIFFRACTIONr_scbond_other2.6931.712993
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3242.4791485
X-RAY DIFFRACTIONr_long_range_B_refined3.38918.1072367
X-RAY DIFFRACTIONr_long_range_B_other3.35217.8622347
X-RAY DIFFRACTIONr_rigid_bond_restr2.73434005
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 142 -
Rwork0.214 2454 -
obs--97.23 %
Refinement TLS params.Method: refined / Origin x: -14.7565 Å / Origin y: 9.5951 Å / Origin z: -14.6057 Å
111213212223313233
T0.009 Å2-0.0088 Å2-0.0034 Å2-0.017 Å20.0037 Å2--0.0016 Å2
L1.0471 °2-0.1433 °2-0.2978 °2-0.9425 °2-0.0876 °2--1.1022 °2
S0.0139 Å °-0.0102 Å °-0.0124 Å °0.0396 Å °-0.0117 Å °-0.0234 Å °0.0413 Å °-0.0026 Å °-0.0022 Å °

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