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- PDB-5f1g: Crystal structure of AmpC BER adenylylated in the cytoplasm -

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Basic information

Entry
Database: PDB / ID: 5f1g
TitleCrystal structure of AmpC BER adenylylated in the cytoplasm
ComponentsBeta-lactamase
KeywordsHYDROLASE / class C beta lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / nucleotide binding / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsAn, Y.J. / Kim, M.K. / Na, J.H. / Cha, S.S.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2015R 1A2A2A 01004168 Korea, Republic Of
National Research Foundation of KoreaNRF-2015M 1A5A 1037480 Korea, Republic Of
KIOST in-house programsPE99314 Korea, Republic Of
KIOST in-house programsPE99302 Korea, Republic Of
CitationJournal: J.Antimicrob.Chemother. / Year: 2017
Title: Structural and mechanistic insights into the inhibition of class C beta-lactamases through the adenylylation of the nucleophilic serine.
Authors: Kim, M.K. / An, Y.J. / Na, J.H. / Seol, J.H. / Ryu, J.Y. / Lee, J.W. / Kang, L.W. / Chung, K.M. / Lee, J.H. / Moon, J.H. / Lee, J.S. / Cha, S.S.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _struct.title
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1235
Polymers40,5561
Non-polymers5674
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-14 kcal/mol
Surface area14510 Å2
Unit cell
Length a, b, c (Å)60.478, 65.414, 106.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase /


Mass: 40556.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: A7TUE6, beta-lactamase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 3.2 / Details: LiSO4, Citric Acid, PEG 3350, MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 42395 / % possible obs: 99.6 % / Redundancy: 11.7 % / Net I/σ(I): 79.18

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3B

1c3b


Resolution: 1.76→32.707 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.55 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 2138 5.05 %
Rwork0.1715 --
obs0.1726 42343 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→32.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 35 259 3051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072875
X-RAY DIFFRACTIONf_angle_d1.1423925
X-RAY DIFFRACTIONf_dihedral_angle_d11.4391028
X-RAY DIFFRACTIONf_chiral_restr0.046420
X-RAY DIFFRACTIONf_plane_restr0.006501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7596-1.80060.2361200.172555X-RAY DIFFRACTION96
1.8006-1.84560.18851580.16192634X-RAY DIFFRACTION100
1.8456-1.89550.20861310.16872673X-RAY DIFFRACTION100
1.8955-1.95120.2051530.16632639X-RAY DIFFRACTION100
1.9512-2.01420.17321510.16242639X-RAY DIFFRACTION100
2.0142-2.08620.19171400.16132654X-RAY DIFFRACTION100
2.0862-2.16970.22911490.16492658X-RAY DIFFRACTION100
2.1697-2.26840.19831390.16542677X-RAY DIFFRACTION100
2.2684-2.3880.20771370.1752662X-RAY DIFFRACTION100
2.388-2.53760.19551440.17352694X-RAY DIFFRACTION100
2.5376-2.73340.22781370.18832681X-RAY DIFFRACTION100
2.7334-3.00830.2171530.18942708X-RAY DIFFRACTION100
3.0083-3.44320.21121270.1842744X-RAY DIFFRACTION100
3.4432-4.33650.17971340.16162759X-RAY DIFFRACTION100
4.3365-32.71260.14471650.16582828X-RAY DIFFRACTION99

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