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- PDB-7mdc: Full-length wildtype ClbP inhibited by hexanoyl-D-asparagine boro... -

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Basic information

Entry
Database: PDB / ID: 7mdc
TitleFull-length wildtype ClbP inhibited by hexanoyl-D-asparagine boronic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / colibactin peptidase / S12 peptidase / boronic acid inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / membrane
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
(2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate / Chem-YX7 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVelilla, J.A. / Volpe, M.R. / Gaudet, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120996 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA208834 United States
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: A small molecule inhibitor prevents gut bacterial genotoxin production.
Authors: Volpe, M.R. / Velilla, J.A. / Daniel-Ivad, M. / Yao, J.J. / Stornetta, A. / Villalta, P.W. / Huang, H.C. / Bachovchin, D.A. / Balbo, S. / Gaudet, R. / Balskus, E.P.
History
DepositionApr 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,71115
Polymers52,9711
Non-polymers3,74114
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SEC-MALS performed on protein solubilized in DDM. Conjugate analysis suggests the average protein molecular weight of the particles in the ClbP peak is approx. 110kDa, ...Evidence: light scattering, SEC-MALS performed on protein solubilized in DDM. Conjugate analysis suggests the average protein molecular weight of the particles in the ClbP peak is approx. 110kDa, which matches the molecular weight of the dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.718, 96.718, 183.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 52970.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clbP / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q0P7K6, beta-lactamase

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Non-polymers , 7 types, 226 molecules

#2: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-97N / (2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate


Mass: 328.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H36O4
#5: Chemical ChemComp-YX7 / [(1S)-3-amino-1-(hexanoylamino)-3-oxopropyl]boronic acid


Mass: 230.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19BN2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.88 Å3/Da / Density % sol: 68.26 % / Description: Square plates grown in a sponge phase
Crystal growTemperature: 295 K / Method: lipidic cubic phase
Details: Precipitant composition: 1 part 0.1M imidazole pH 7.8, 10% (v/v) PEG 400, 150 mM Li2SO4, 11 mM (S)-N-(3-amino-3-oxo-1-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)propyl)hexanamide plus 3.5 ...Details: Precipitant composition: 1 part 0.1M imidazole pH 7.8, 10% (v/v) PEG 400, 150 mM Li2SO4, 11 mM (S)-N-(3-amino-3-oxo-1-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)propyl)hexanamide plus 3.5 parts 0.1M tris pH 7.2, 25%(v/v) PEG400, 200 mM Li2SO4
PH range: 7.2-7.8 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryojet cryocooler / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→45.58 Å / Num. obs: 24663 / % possible obs: 99.88 % / Redundancy: 10.9 % / Biso Wilson estimate: 48.5 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2575 / Rpim(I) all: 0.08088 / Rrim(I) all: 0.2702 / Net I/σ(I): 8.06
Reflection shellResolution: 2.7→2.797 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.887 / Num. unique obs: 2389 / CC1/2: 0.534 / CC star: 0.834 / Rpim(I) all: 0.5802 / Rrim(I) all: 1.975 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
DIALS1.14.5-g19190e3b9-releasedata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MDE

7mde


Resolution: 2.7→45.58 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2359 1231 4.99 %
Rwork0.1926 23414 -
obs-24644 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.88 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 108 212 3635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713482
X-RAY DIFFRACTIONf_angle_d0.92224714
X-RAY DIFFRACTIONf_chiral_restr0.0518540
X-RAY DIFFRACTIONf_plane_restr0.0082596
X-RAY DIFFRACTIONf_dihedral_angle_d21.06491238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.810.3651320.29892534X-RAY DIFFRACTION99.93
2.81-2.940.30081350.24662546X-RAY DIFFRACTION100
2.94-3.090.27851340.23532555X-RAY DIFFRACTION99.85
3.09-3.280.27831340.2182558X-RAY DIFFRACTION99.96
3.28-3.540.25911360.18852572X-RAY DIFFRACTION99.89
3.54-3.890.18531350.16322585X-RAY DIFFRACTION100
3.89-4.460.20171390.14692611X-RAY DIFFRACTION100
4.46-5.610.20311370.16832647X-RAY DIFFRACTION99.96
5.61-45.580.23981490.20012806X-RAY DIFFRACTION99.66
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.65130517603-0.2406775561130.2410369436862.41911821161-0.4852130540732.515612623450.0447576375609-0.07963964199990.1682417562730.0589077440501-0.139269692682-0.284849143124-0.0436383279150.2007267175740.009824368279320.3272913103530.03071559817340.03491290009260.3882318248920.02394897414780.56538355496823.18030180333.768663562349.1672583961
21.733913437530.1379146176390.1896971697321.16885619712-0.297255209421.202044618380.01088497798930.03497212744180.144832348714-0.13794667856-0.02700089294440.3023511039060.0206366169324-0.247475775239-0.01576903569980.3190559177740.01227855177030.01143064272690.361175212759-0.001979593445140.668032920937-11.076237029624.918640829145.1498381833
33.59570131235-0.2231559791710.6143688140230.7019560141130.672108012042.18439786689-0.14184327661-0.396655525126-0.1889829995560.5762649599190.2093239363920.450804634380.175018416097-0.168234230817-0.05129641029980.38616706663-0.01477862786320.0204598912550.4360657082460.03597285535760.622475507119-9.7462940074226.00795602157.3027856664
41.91285238777-0.4336412254810.5127497727481.222334872790.1988909538661.210373355560.055858156356-0.0849312216198-0.3809822988780.0182020688612-0.00760578281820.04270842939950.2883854265840.0788874232158-0.07980124959540.3225301210670.009919067372940.03048314539980.326755346340.02345849545930.6768435500677.5514787749821.150545711149.2362467677
52.04773906340.1508419522430.1691229161892.093013775420.699438316811.071024782080.2767664005270.735719227740.139841042703-0.586270669933-0.1908818185320.0587997131092-0.328067261965-0.0882122052960.03467543346160.346341444276-0.0160658588221-0.03453101942070.4448609147190.03815256849240.641920552081-1.0648482216432.294540237633.9445277444
61.212850244070.05476437229260.3719498604861.14535432496-0.9285070242540.906704503028-0.0188802507015-0.1195892525790.4989445691440.1099832010210.03590541126470.1094620722-0.2487672009060.04936613799360.03192071842730.293344322124-0.003190027613210.02568287119170.358953163522-0.03854944557250.5191427319899.557365174940.117438582946.0392012704
71.842254159270.1425608654110.9312474456561.5727799029-0.1843642354641.856182896530.133698823366-0.338050300550.4349739410050.704441463926-0.3268814639490.18924468954-0.428723224813-0.1531548627160.0349374728860.781478933111-0.153680215757-0.01356274253210.670832667135-0.1341038145150.61468072529111.815499039840.729389354682.8277514009
82.044069877561.61039229461.149705706961.847195848650.8229760547050.6563116911310.766001499295-1.305422440070.1703128728060.739200370973-0.4148286324790.2985118231440.553210084343-0.5768269486910.3609041643610.906448333182-0.1406267925420.2807849553391.24436739351-0.2583024489120.557446572317-1.7054272282830.450565091389.0721762936
91.46962844824-0.167107561481-0.001815221302571.581978557130.1795424994623.42045973667-0.0510235236657-0.654745337409-0.5449691875890.460653124425-0.1506551763540.3192549630440.533947156817-0.3693988862340.0650984672940.599927719451-0.03989549310950.0110621333740.8672152888270.2032982746060.6255733841493.5725462447231.922571967180.8714560411
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 36 through 93 )36 - 931 - 58
22chain 'A' and (resid 94 through 151)94 - 15159 - 116
33chain 'A' and (resid 152 through 187 )152 - 187117 - 152
44chain 'A' and (resid 188 through 278 )188 - 278153 - 243
55chain 'A' and (resid 279 through 305 )279 - 305244 - 270
66chain 'A' and (resid 306 through 381 )306 - 381271 - 346
77chain 'A' and (resid 382 through 408 )382 - 408347 - 373
88chain 'A' and (resid 409 through 454 )409 - 454374 - 401
99chain 'A' and (resid 455 through 491 )455 - 491402 - 438

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