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- PDB-8r88: Structure of P107T BlaC from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8r88
TitleStructure of P107T 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
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChikunova, A. / Ubbink, M.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Protein Sci. / Year: 2024
Title: Conserved proline residues prevent dimerization and aggregation in the beta-lactamase BlaC.
Authors: Chikunova, A. / Manley, M.P. / Heijjer, C.N. / Drenth, C.S. / Cramer-Blok, A.J. / Ahmad, M.U.D. / Perrakis, A. / Ubbink, M.
History
DepositionNov 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,86112
Polymers113,1074
Non-polymers7548
Water8,557475
1
A: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9306
Polymers56,5532
Non-polymers3774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-31 kcal/mol
Surface area19230 Å2
2
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9306
Polymers56,5532
Non-polymers3774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-31 kcal/mol
Surface area19150 Å2
Unit cell
Length a, b, c (Å)47.002, 70.616, 124.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase


Mass: 28276.713 Da / Num. of mol.: 4 / Mutation: P107T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A655AHQ9
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / 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: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 1.91 Å3/Da / Density % sol: 35.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MB1 (pH 6.5), 0.06 M divalent, 30 %w/v 550M_20K

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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: 1.95→124.59 Å / Num. obs: 58924 / % possible obs: 99 % / Redundancy: 1.9 % / CC1/2: 0.995 / Net I/σ(I): 8.6
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3969 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→124.59 Å / SU B: 7.955 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.154 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 2928 5 %RANDOM
Rwork0.16994 ---
obs0.17153 55982 98.81 %-
Displacement parametersBiso mean: 14.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-0 Å20.04 Å2
2--1.1 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.95→124.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7610 0 42 475 8127

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