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- PDB-5gzw: Crystal structure of AmpC BER adenylylated by acetyl-AMP -

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Basic information

Entry
Database: PDB / ID: 5gzw
TitleCrystal structure of AmpC BER adenylylated by acetyl-AMP
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / Class C / AmpC
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / nucleotide binding
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 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 Å
AuthorsAn, Y.J. / Cha, S.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
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
DepositionOct 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,9035
Polymers81,1122
Non-polymers7913
Water6,666370
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9032
Polymers40,5561
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9993
Polymers40,5561
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.480, 65.039, 177.271
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.: 2
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, UniProt: A0A076YIY5*PLUS, beta-lactamase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.5
Details: 0.2M Lithium sulfate, 0.1M Bis-tris pH 5.5, 25% polyethylene glycol 3500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.489→50 Å / Num. obs: 115016 / % possible obs: 98.3 % / Redundancy: 5.1 % / Net I/σ(I): 32
Reflection shellResolution: 1.49→1.52 Å

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Processing

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

1c3b


Resolution: 1.489→44.678 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 24.97
RfactorNum. reflection% reflection
Rfree0.2371 5755 5 %
Rwork0.2107 --
obs0.2121 115015 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.489→44.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 49 370 5869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075666
X-RAY DIFFRACTIONf_angle_d1.1677742
X-RAY DIFFRACTIONf_dihedral_angle_d12.7282026
X-RAY DIFFRACTIONf_chiral_restr0.078832
X-RAY DIFFRACTIONf_plane_restr0.006988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4891-1.5060.37282000.36393267X-RAY DIFFRACTION90
1.506-1.52370.41830.34673512X-RAY DIFFRACTION97
1.5237-1.54230.33531850.3393580X-RAY DIFFRACTION97
1.5423-1.56180.34181740.31923533X-RAY DIFFRACTION97
1.5618-1.58240.32681840.30593560X-RAY DIFFRACTION97
1.5824-1.6040.28081920.29533549X-RAY DIFFRACTION97
1.604-1.6270.35981780.29373624X-RAY DIFFRACTION97
1.627-1.65130.3022090.27213524X-RAY DIFFRACTION98
1.6513-1.67710.28741930.25933604X-RAY DIFFRACTION98
1.6771-1.70460.29462060.253595X-RAY DIFFRACTION98
1.7046-1.73390.26532020.24423599X-RAY DIFFRACTION98
1.7339-1.76550.25971960.23093611X-RAY DIFFRACTION98
1.7655-1.79940.251810.21883640X-RAY DIFFRACTION99
1.7994-1.83620.24321650.20823651X-RAY DIFFRACTION99
1.8362-1.87610.24771950.21263634X-RAY DIFFRACTION98
1.8761-1.91970.2641990.2133641X-RAY DIFFRACTION99
1.9197-1.96770.24781900.21393662X-RAY DIFFRACTION99
1.9677-2.02090.22851950.20593653X-RAY DIFFRACTION99
2.0209-2.08040.23871820.20423682X-RAY DIFFRACTION99
2.0804-2.14760.23271960.20533644X-RAY DIFFRACTION99
2.1476-2.22430.23521830.2043680X-RAY DIFFRACTION99
2.2243-2.31340.2531730.2023710X-RAY DIFFRACTION99
2.3134-2.41860.24581650.20963735X-RAY DIFFRACTION100
2.4186-2.54620.22551980.2113691X-RAY DIFFRACTION100
2.5462-2.70570.23842050.21663718X-RAY DIFFRACTION100
2.7057-2.91450.26242180.21733709X-RAY DIFFRACTION100
2.9145-3.20780.24182020.2153745X-RAY DIFFRACTION100
3.2078-3.67170.23811740.19913800X-RAY DIFFRACTION100
3.6717-4.62520.17852160.16153805X-RAY DIFFRACTION100
4.6252-44.69830.17372160.16913902X-RAY DIFFRACTION98

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