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- PDB-6k8x: Crystal structure of a class C beta lactamase -

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Basic information

Entry
Database: PDB / ID: 6k8x
TitleCrystal structure of a class C beta lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / ACC1 class C Beta-lactamase
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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 13, 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 22, 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


Theoretical massNumber of molelcules
Total (without water)40,7131
Polymers40,7131
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15060 Å2
Unit cell
Length a, b, c (Å)133.160, 60.290, 56.215
Angle α, β, γ (deg.)90.000, 111.990, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
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: 1.2826 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 51126 / % possible obs: 91.9 % / Redundancy: 4 % / Biso Wilson estimate: 14.58 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.043 / Rrim(I) all: 0.089 / Χ2: 4.224 / Net I/σ(I): 18.9 / Num. measured all: 206207
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.59-1.623.70.2326460.9450.1380.273.4196.8
1.62-1.653.90.21927300.950.1280.2553.47598.2
1.65-1.6840.19327360.970.110.2233.60998.4
1.68-1.7140.17526980.9650.0990.2033.5998
1.71-1.753.90.1727120.9580.0970.1973.93897.4
1.75-1.7940.14827010.970.0840.1713.78397.9
1.79-1.844.60.13627480.9790.0730.1553.87598.9
1.84-1.894.40.12927240.9730.0710.1483.97198.6
1.89-1.943.10.12122070.9710.0760.1444.37179.5
1.94-240.10626580.9820.0610.1234.44596.5
2-2.073.60.09724660.9830.0580.1144.57888.8
2.07-2.164.10.09126480.9880.0510.1044.71194.4
2.16-2.2640.08424240.9890.0470.0974.7187.7
2.26-2.384.20.08125390.9880.0450.0934.78591.3
2.38-2.524.40.07626860.990.0420.0884.80196.4
2.52-2.723.70.07425460.9890.0420.0864.89991.5
2.72-2.994.60.06826820.990.0360.0774.69396.4
2.99-3.434.30.06224930.9910.0330.0714.50988.8
3.43-4.322.90.05315780.9920.0330.0634.3255.9
4.32-504.70.05425040.9930.0280.0614.15887.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ixh

3ixh


Resolution: 1.59→34.814 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.56 / Phase error: 18.9
RfactorNum. reflection% reflection
Rfree0.2072 2590 5.07 %
Rwork0.1835 --
obs0.1847 51117 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.43 Å2 / Biso mean: 19.0398 Å2 / Biso min: 7.58 Å2
Refinement stepCycle: final / Resolution: 1.59→34.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 0 220 2953
Biso mean---26.26 -
Num. residues----356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5883-1.61720.22581260.23252559268592
1.6172-1.64830.24051410.20292736287798
1.6483-1.6820.25841450.19122726287198
1.682-1.71850.22241400.19162714285498
1.7185-1.75850.21631490.19052698284798
1.7585-1.80250.23561470.18472712285998
1.8025-1.85120.19431440.18512747289199
1.8512-1.90570.21151460.18282712285898
1.9057-1.96720.23611230.20842198232179
1.9672-2.03750.20381500.17442720287098
2.0375-2.11910.20821200.18222385250586
2.1191-2.21550.18051430.16922760290399
2.2155-2.33230.19881170.18182271238882
2.3323-2.47840.19741340.17412700283497
2.4784-2.66960.19141590.18212605276494
2.6696-2.93820.23671520.18692622277494
2.9382-3.3630.22851380.18652634277294
3.363-4.23590.2021850.19461526161154
4.2359-34.82240.17311310.1692502263387

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