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- PDB-6dpt: X-ray crystal structure of AmpC beta-lactamase with nanomolar inh... -

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Basic information

Entry
Database: PDB / ID: 6dpt
TitleX-ray crystal structure of AmpC beta-lactamase with nanomolar inhibitor
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE Inhibitor / AmpC beta-lacatamase / inhibitor complex / phenolate / 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
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H7M / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsSingh, I.
CitationJournal: Nature / Year: 2019
Title: Ultra-large library docking for discovering new chemotypes.
Authors: Lyu, J. / Wang, S. / Balius, T.E. / Singh, I. / Levit, A. / Moroz, Y.S. / O'Meara, M.J. / Che, T. / Algaa, E. / Tolmachova, K. / Tolmachev, A.A. / Shoichet, B.K. / Roth, B.L. / Irwin, J.J.
History
DepositionJun 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
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 1.2Oct 11, 2023Group: 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
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9704
Polymers79,1762
Non-polymers7942
Water4,846269
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9852
Polymers39,5881
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9852
Polymers39,5881
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.166, 77.557, 115.510
Angle α, β, γ (deg.)90.000, 113.040, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ampC, ampA, b4150, JW4111 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-H7M / 3-chloro-2-hydroxy-N-{2-[(4-methyl-4H-1,2,4-triazol-3-yl)sulfanyl]phenyl}benzene-1-sulfonamide


Mass: 396.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13ClN4O3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 1.7 M potassium phosphate, pH 8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.79→87.87 Å / Num. obs: 75002 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Net I/σ(I): 13.5
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4399 / CC1/2: 0.613 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KE4

1ke4


Resolution: 1.79→87.866 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2191 3766 5.02 %
Rwork0.1869 --
obs0.1885 74955 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.58 Å2 / Biso mean: 34.808 Å2 / Biso min: 18.44 Å2
Refinement stepCycle: final / Resolution: 1.79→87.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5493 0 50 269 5812
Biso mean--42.64 38.55 -
Num. residues----716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075718
X-RAY DIFFRACTIONf_angle_d0.8677841
X-RAY DIFFRACTIONf_chiral_restr0.053855
X-RAY DIFFRACTIONf_plane_restr0.0051007
X-RAY DIFFRACTIONf_dihedral_angle_d4.2333933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.79-1.81270.35951300.32512609273999
1.8127-1.83650.30581310.301226292760100
1.8365-1.86170.29071520.279226282780100
1.8617-1.88830.30781340.264726092743100
1.8883-1.91650.30371430.292826552798100
1.9165-1.94640.36631630.281825652728100
1.9464-1.97830.23611550.231726282783100
1.9783-2.01240.2791540.214426052759100
2.0124-2.0490.25321420.215526412783100
2.049-2.08840.27431320.209426582790100
2.0884-2.13110.23391570.212325852742100
2.1311-2.17740.2481330.206526462779100
2.1774-2.22810.22381480.21126242772100
2.2281-2.28380.33121370.24282641277899
2.2838-2.34560.25741350.210226112746100
2.3456-2.41460.23061400.226722812100
2.4146-2.49250.22521520.193725962748100
2.4925-2.58160.25941270.205426692796100
2.5816-2.6850.21681450.197626152760100
2.685-2.80720.24071580.204726242782100
2.8072-2.95520.22821220.207826932815100
2.9552-3.14040.23151300.198226382768100
3.1404-3.38280.23891290.19732665279499
3.3828-3.72330.18951400.16326352775100
3.7233-4.2620.17751230.14222651277499
4.262-5.36960.15351200.13752681280199
5.3696-87.97240.1671340.1592716285099

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