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- PDB-6kby: Crystal structure of a class C beta lactamase in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 6kby
TitleCrystal structure of a class C beta lactamase in complex with AMP
ComponentsBeta-lactamase
KeywordsHYDROLASE / Crystal structures / Class C beta-lactamase / Acyl-enzyme complex / AMP
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.097 Å
AuthorsBae, D.W. / Jung, Y.E. / An, Y.J. / Na, J.H. / Cha, S.S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Structural Insights into Catalytic Relevances of Substrate Poses in ACC-1.
Authors: Bae, D.W. / Jung, Y.E. / An, Y.J. / Na, J.H. / Cha, S.S.
History
DepositionJun 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)41,0612
Polymers40,7131
Non-polymers3471
Water9,314517
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-2 kcal/mol
Surface area15280 Å2
Unit cell
Length a, b, c (Å)132.270, 60.230, 56.140
Angle α, β, γ (deg.)90.000, 112.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase


Mass: 40713.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla-ACC-1, acc-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XB24, beta-lactamase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.1M sodium cacodylate pH 5.5, 0.2M sodium chloride, 35% polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 26, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.097→41.036 Å / Num. obs: 165696 / % possible obs: 99.32 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Rsym value: 0.058 / Net I/σ(I): 13.21
Reflection shellResolution: 1.097→1.102 Å / Num. unique obs: 12228 / Rsym value: 0.694

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.097→41.036 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.13
RfactorNum. reflection% reflection
Rfree0.1812 1991 1.2 %
Rwork0.1689 --
obs0.169 165622 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 38.99 Å2 / Biso mean: 12.9569 Å2 / Biso min: 5.01 Å2
Refinement stepCycle: final / Resolution: 1.097→41.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 22 517 3325
Biso mean--16.4 21.57 -
Num. residues----362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042871
X-RAY DIFFRACTIONf_angle_d0.863903
X-RAY DIFFRACTIONf_chiral_restr0.083445
X-RAY DIFFRACTIONf_plane_restr0.006496
X-RAY DIFFRACTIONf_dihedral_angle_d15.6811050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.097-1.12440.25791260.2586114351156198
1.1244-1.15480.22191450.22114841162998
1.1548-1.18880.2331490.2093115471169699
1.1888-1.22720.1961480.1918116221177099
1.2272-1.27110.18771410.1825116261176799
1.2711-1.32190.17491380.1696116541179299
1.3219-1.38210.1771520.16571166411816100
1.3821-1.4550.18071370.16351174011877100
1.455-1.54610.17051470.15661174611893100
1.5461-1.66550.16671390.15431174211881100
1.6655-1.83310.18171520.16361177811930100
1.8331-2.09840.20211440.15961177011914100
2.0984-2.64370.17291370.16821185011987100
2.6437-41.06470.16381360.16061197312109100

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