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- PDB-6k9t: Crystal structure of a class C beta-lactamase in complex with cef... -

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Basic information

Entry
Database: PDB / ID: 6k9t
TitleCrystal structure of a class C beta-lactamase in complex with cefotaxime
ComponentsBeta-lactamase
KeywordsHYDROLASE / ACC-1 class C beta-lactamase / Acyl-enzyme complex / Cefotaxime
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
CEFOTAXIME, C3' cleaved, open, bound form / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.459 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 17, 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 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model

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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)41,1112
Polymers40,7131
Non-polymers3971
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-1 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.219, 60.416, 56.039
Angle α, β, γ (deg.)90.000, 111.980, 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-CEF / CEFOTAXIME, C3' cleaved, open, bound form / Cefotaxime


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.11 %
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: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.2825 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 65261 / % possible obs: 91.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 11.71 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.038 / Rrim(I) all: 0.092 / Χ2: 3.226 / Net I/σ(I): 15.9 / Num. measured all: 382190
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.46-1.496.10.51933040.9350.2270.5682.09893.2
1.49-1.516.20.46134050.9470.20.5032.26294.8
1.51-1.5460.433890.9670.1790.4392.42895
1.54-1.575.80.34533400.9680.1580.382.56694.9
1.57-1.615.50.28734480.9650.1360.3182.59895.3
1.61-1.645.70.26333930.9660.1210.292.77895.7
1.64-1.696.10.2134450.9790.0930.232.87596
1.69-1.736.20.17634260.9860.0770.1922.80696.3
1.73-1.786.20.15234450.9870.0660.1662.96696.7
1.78-1.845.90.13434620.9880.060.1473.22196.8
1.84-1.9160.12232800.9890.0540.1343.49892.1
1.91-1.986.10.10221790.9930.0440.1123.80461
1.98-2.076.10.0934760.9940.0390.0983.95897
2.07-2.185.90.08334900.9940.0370.0914.16997.5
2.18-2.3250.07222620.9940.0340.084.10163.1
2.32-2.560.06935430.9960.030.0753.99998.3
2.5-2.755.90.06335260.9960.0280.0693.89498.2
2.75-3.155.30.05835390.9950.0270.0653.86698.1
3.15-3.965.10.05223280.9950.0240.0583.72864.2
3.96-505.50.05235810.9960.0240.0573.7397

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.459→26.116 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1898 3246 4.97 %
Rwork0.1685 62009 -
obs0.1696 65255 90.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.36 Å2 / Biso mean: 15.577 Å2 / Biso min: 5.84 Å2
Refinement stepCycle: final / Resolution: 1.459→26.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 26 234 2991
Biso mean--22.64 22.97 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182818
X-RAY DIFFRACTIONf_angle_d1.7743834
X-RAY DIFFRACTIONf_chiral_restr0.093440
X-RAY DIFFRACTIONf_plane_restr0.01488
X-RAY DIFFRACTIONf_dihedral_angle_d13.7811017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.459-1.48080.22171360.18452666280289
1.4808-1.5040.24741300.19762744287494
1.504-1.52860.2841460.20462799294595
1.5286-1.5550.25631410.20862859300095
1.555-1.58320.21451450.20462804294995
1.5832-1.61370.20671580.19792769292795
1.6137-1.64660.2261350.19742871300696
1.6466-1.68240.19451060.17342871297796
1.6824-1.72150.18611310.16322847297896
1.7215-1.76460.20171520.15372848300096
1.7646-1.81230.1891370.14962850298797
1.8123-1.86560.20071280.15422917304597
1.8656-1.92580.2055910.15591753184490
1.9258-1.99460.16261320.15872589272189
1.9946-2.07440.16161570.15452879303697
2.0744-2.16880.18091500.16352899304998
2.1688-2.28310.201840.16741736182058
2.2831-2.4260.19821650.16722908307398
2.426-2.61320.17771890.16832868305798
2.6132-2.87590.16492090.17412868307798
2.8759-3.29130.20761640.17912928309298
3.2913-4.1440.1962870.16251765185259
4.144-26.12010.16781730.15572971314497

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