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- PDB-6dpz: X-ray crystal structure of AmpC beta-lactamase with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6dpz
TitleX-ray crystal structure of AmpC beta-lactamase with inhibitor
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE Inhibitor / AmpC beta-lacatamase / inhibitor complex / 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-H7D / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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)79,7854
Polymers79,1762
Non-polymers6092
Water10,683593
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8922
Polymers39,5881
Non-polymers3041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8922
Polymers39,5881
Non-polymers3041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.702, 77.737, 115.686
Angle α, β, γ (deg.)90.000, 113.250, 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-H7D / (1R,2S)-2-{[(pyrrolidin-1-yl)sulfonyl]amino}cyclooctane-1-carboxylic acid


Mass: 304.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H24N2O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 1.7M potassium phosphate / PH range: 8.9

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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: 1.5→62.75 Å / Num. obs: 126380 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Net I/σ(I): 13.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.718 / Num. unique obs: 6182 / CC1/2: 0.529 / Rpim(I) all: 0.727 / Rrim(I) all: 1.869 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KE4

1ke4


Resolution: 1.5→62.746 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2233 6323 5.01 %
Rwork0.1914 --
obs0.193 126187 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.16 Å2 / Biso mean: 30.228 Å2 / Biso min: 15.95 Å2
Refinement stepCycle: final / Resolution: 1.5→62.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5491 0 40 593 6124
Biso mean--35.4 37.86 -
Num. residues----716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075706
X-RAY DIFFRACTIONf_angle_d0.9317820
X-RAY DIFFRACTIONf_chiral_restr0.054863
X-RAY DIFFRACTIONf_plane_restr0.0061002
X-RAY DIFFRACTIONf_dihedral_angle_d4.6673959
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51710.3222280.33023935416399
1.5171-1.53490.3612040.32243923412799
1.5349-1.55360.32072120.31053948416098
1.5536-1.57330.32522320.28864016424899
1.5733-1.5940.34262050.283933413899
1.594-1.61580.29952090.27853967417699
1.6158-1.63890.29772180.25833981419999
1.6389-1.66340.27942080.25373923413199
1.6634-1.68940.3082030.24754045424899
1.6894-1.71710.2761850.238239814166100
1.7171-1.74670.26172000.24413994419499
1.7467-1.77850.28392120.23564011422399
1.7785-1.81270.2722120.22914008422099
1.8127-1.84970.25672270.227339434170100
1.8497-1.88990.24321970.238440264223100
1.8899-1.93390.34151800.28583997417799
1.9339-1.98220.2471950.217140324227100
1.9822-2.03580.22312140.207940194233100
2.0358-2.09570.2372480.208939714219100
2.0957-2.16340.24122050.202140394244100
2.1634-2.24070.22282080.21253947415599
2.2407-2.33040.26172210.223960418199
2.3304-2.43650.20642010.197840504251100
2.4365-2.56490.24142190.196940114230100
2.5649-2.72560.24481940.197240534247100
2.7256-2.93610.21982040.194540274231100
2.9361-3.23150.23042170.18243988420599
3.2315-3.69910.20592180.16294022424099
3.6991-4.66030.15992170.141440424259100
4.6603-62.80070.19252300.15774072430299

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