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- PDB-7pa5: Complex between the beta-lactamase CMY-2 with an inhibitory nanobody -

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Basic information

Entry
Database: PDB / ID: 7pa5
TitleComplex between the beta-lactamase CMY-2 with an inhibitory nanobody
Components
  • Beta-lactamase
  • nanobody
KeywordsHYDROLASE / Single Domain Camelid Antibody Cephalosporinase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.184 Å
AuthorsFrederic Cawez, F.C. / Frederic Kerff, F.K. / Moreno Galleni, M.G. / Raphael Herman, R.H.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2023
Title: Development of Nanobodies as Theranostic Agents against CMY-2-Like Class C beta-Lactamases.
Authors: Cawez, F. / Mercuri, P.S. / Morales-Yanez, F.J. / Maalouf, R. / Vandevenne, M. / Kerff, F. / Guerin, V. / Mainil, J. / Thiry, D. / Saulmont, M. / Vanderplasschen, A. / Lafaye, P. / Ayme, G. ...Authors: Cawez, F. / Mercuri, P.S. / Morales-Yanez, F.J. / Maalouf, R. / Vandevenne, M. / Kerff, F. / Guerin, V. / Mainil, J. / Thiry, D. / Saulmont, M. / Vanderplasschen, A. / Lafaye, P. / Ayme, G. / Bogaerts, P. / Dumoulin, M. / Galleni, M.
History
DepositionJul 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2914
Polymers54,1042
Non-polymers1872
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-8 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.120, 95.120, 242.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11B-201-

PO4

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Components

#1: Protein Beta-lactamase


Mass: 39896.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: bla CMY-2, ampC, blaCMY-2, blacmy-2, blaCMY-2-1, CMY-2, cmy-2, A9819_28690, AM333_27370, AM464_28260, APX88_19125, BB545_24720, BHS81_30845, BIQ87_27420, BIU72_25045, BK248_14575, BK292_11440, ...Gene: bla CMY-2, ampC, blaCMY-2, blacmy-2, blaCMY-2-1, CMY-2, cmy-2, A9819_28690, AM333_27370, AM464_28260, APX88_19125, BB545_24720, BHS81_30845, BIQ87_27420, BIU72_25045, BK248_14575, BK292_11440, BK375_28010, BWI89_23710, CWM24_03220, D2184_22885, D2185_19815, D2188_23590, D9D43_21375, D9D43_30790, DS732_29990, E2129_13225, EAN77_15185, ED648_23630, ED648_28285, EJC75_03830, EJC75_22930, ELT58_15290, EO241_21750, FKC84_16435, HMQ05_23325, HMQ05_27045, HND23_22080, HND23_27950, HVX28_23930, HVZ20_24300, HVZ21_14455, KPCE_053, pAPEC1990_61_74, pAR060302_0084, pAR060302_81, peH4H_0073, pESCR_00001, WR15_23065
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53TY8, beta-lactamase
#2: Antibody nanobody


Mass: 14207.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG400, glycerol, Ammonium tartarate, tris HCl,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.18→48.885 Å / Num. obs: 11589 / % possible obs: 99.6 % / Redundancy: 37.789 % / Biso Wilson estimate: 76.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.709 / Rrim(I) all: 0.719 / Χ2: 0.599 / Net I/σ(I): 7.09 / Num. measured all: 437933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.18-3.3734.7613.4261.2861109179617580.4293.47797.9
3.37-3.639.9372.1092.5168292171017100.9052.136100
3.6-3.8940.5131.6763.5764902160216020.9141.697100
3.89-4.2639.4241.0215.558623148714870.9791.034100
4.26-4.7636.850.6657.9350743137713770.9880.675100
4.76-5.4937.9340.5189.3945672120412040.9950.525100
5.49-6.739.0270.45410.3141134105410540.9950.46100
6.7-9.3835.2860.20417.05300288518510.9990.207100
9.38-48.88531.9230.12925.841743055154610.13199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.18 Å48.88 Å
Translation3.18 Å48.88 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZC2 (CMY-2), 6GKU (nanobody)

1zc2

6gku


Resolution: 3.184→48.885 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 576 5 %
Rwork0.2067 10942 -
obs0.209 11518 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.84 Å2 / Biso mean: 78.8152 Å2 / Biso min: 38.08 Å2
Refinement stepCycle: final / Resolution: 3.184→48.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 19 8 3770
Biso mean--80.41 52.03 -
Num. residues----481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.184-3.5040.35521370.2695260598
3.504-4.01080.26591410.21462679100
4.0108-5.05240.20861440.17532734100
5.0524-48.8850.23651540.20542924100

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