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- PDB-6huh: CRYSTAL STRUCTURE OF OXA-427 class D BETA-LACTAMASE -

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Basic information

Entry
Database: PDB / ID: 6huh
TitleCRYSTAL STRUCTURE OF OXA-427 class D BETA-LACTAMASE
ComponentsBeta-lactamase
KeywordsHYDROLASE / CLASS D BETA-LACTAMASE OXA-427-HisTag / ANTIBIOTIC / DIMER
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / 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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsZavala, A. / Retailleau, P. / Bogaerts, P. / Glupczynski, Y. / Naas, T. / Iorga, B.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-33 France
French National Research AgencyANR-14-JAMR-0002 France
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF CMY-OXA-427-HisTag BETA-LACTAMASE
Authors: Zavala, A. / Naas, T. / Bogaerts, P. / Glupczynski, Y. / Retailleau, P. / Iorga, B.I.
History
DepositionOct 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2875
Polymers60,9992
Non-polymers2883
Water2,414134
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-35 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.790, 42.580, 99.710
Angle α, β, γ (deg.)90.00, 114.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

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Components

#1: Protein Beta-lactamase


Mass: 30499.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA-427, PKLPN57_278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y6M6D7, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.2M ammonium sulfate; 0.2M sodium fluoride

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
21001N
11001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 220.9801
SYNCHROTRONSOLEIL PROXIMA 210.9801
Detector
TypeIDDetectorDate
DECTRIS EIGER X 9M2PIXELApr 8, 2017
DECTRIS EIGER X 9M1PIXELApr 8, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2SINGLE WAVELENGTHMx-ray1
1SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.98011
20.98011
ReflectionResolution: 2.776→68.1 Å / Num. obs: 13454 / % possible obs: 94.2 % / Redundancy: 3 % / Biso Wilson estimate: 56.79 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.2
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSv20160617data reduction
Aimlessv0.5.31data scaling
MrBUMPv7.0.027phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GN2

4gn2


Resolution: 2.78→68.1 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.854 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.41
RfactorNum. reflection% reflectionSelection details
Rfree0.269 681 5.09 %RANDOM
Rwork0.205 ---
obs0.208 13388 94.2 %-
Displacement parametersBiso mean: 50.21 Å2
Baniso -1Baniso -2Baniso -3
1-5.7283 Å20 Å29.2821 Å2
2--8.1414 Å20 Å2
3----13.8697 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.78→68.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 37 134 3961
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013942HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.175349HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1310SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes566HARMONIC5
X-RAY DIFFRACTIONt_it3942HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion22.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion486SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4536SEMIHARMONIC4
LS refinement shellResolution: 2.78→3 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2892 154 5.33 %
Rwork0.2128 2738 -
all0.2166 2892 -
obs--99.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6946-0.34621.17971.7313-0.78051.4716-0.05380.06950.13390.05140.04560.02180.11260.02290.0082-0.0384-0.0108-0.1085-0.1050.0229-0.142717.770624.37337.5835
22.3854-0.12271.71872.1928-0.42512.46390.11180.1142-0.01850.03820.0256-0.01020.11240.1435-0.1373-0.00260.0812-0.2224-0.1734-0.037-0.176441.634539.673528.4623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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