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- PDB-7l5t: Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-s... -

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Basic information

Entry
Database: PDB / ID: 7l5t
TitleCrystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase OXA-14 from Pseudomonas aeruginosa in Complex with Covalently Bound Clavulanic Acid
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Class D Beta-lactamase / OXA-14 / Clavulanic Acid / Center for Membrane Proteins of Infectious Diseases / MPID / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / 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/transpeptidase-like
Similarity search - Domain/homology
(2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMinasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Brunzelle, J.S. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Membrane Proteins of Infectious Diseases (MPID)
CitationJournal: To Be Published
Title: Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase OXA-14 from Pseudomonas aeruginosa in Complex with Covalently Bound Clavulanic Acid
Authors: Minasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Brunzelle, J.S. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,47921
Polymers55,6532
Non-polymers1,82619
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-187 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.940, 95.451, 125.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / OXA-14 Beta-lactamase


Mass: 27826.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: OXA-14, blaOXA / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 Magic / References: UniProt: Q59648, beta-lactamase
#2: Chemical ChemComp-ISS / (2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal


Mass: 157.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein: 8.0 mg/ml, 0.01M Tris pH 8.3; Screen - AmSO4 (F6): 0.1M Bicine pH 9.0, 2.4M Ammonium sulfate; Soak & Cryo: 50mM Clavulanic acid, 2M Lithium sulfate, 10 min
PH range: 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 13, 2020 / Details: Be
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 48753 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Rrim(I) all: 0.077 / Rsym value: 0.071 / Χ2: 1.004 / Net I/σ(I): 25.3
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2374 / CC1/2: 0.848 / CC star: 0.958 / Rpim(I) all: 0.36 / Rrim(I) all: 0.916 / Rsym value: 0.841 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3U

1e3u


Resolution: 1.88→29.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.389 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2457 5 %RANDOM
Rwork0.1672 ---
obs0.1687 46232 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.01 Å2 / Biso mean: 31.172 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--2.16 Å2-0 Å2
3----2.47 Å2
Refinement stepCycle: final / Resolution: 1.88→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 116 358 4376
Biso mean--75.37 36.31 -
Num. residues----493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134109
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173737
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.6315560
X-RAY DIFFRACTIONr_angle_other_deg0.3731.5738708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7535497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31123.463205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.8715714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9271516
X-RAY DIFFRACTIONr_chiral_restr0.0660.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.024509
X-RAY DIFFRACTIONr_gen_planes_other0.050.02831
LS refinement shellResolution: 1.881→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 181 -
Rwork0.229 3275 -
all-3456 -
obs--98.57 %
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)
14.1225-2.00610.69072.83650.32022.15-0.08780.2245-0.4291-0.1227-0.02530.35310.3771-0.16920.11310.1657-0.049-0.00490.0649-0.06120.1061-19.2994-3.5638-13.2504
20.8130.35280.64731.12080.88272.8788-0.04470.1341-0.0181-0.0550.0495-0.05690.03830.1536-0.00480.0217-0.01040.00360.0278-0.01060.0622-10.49749.0314-4.8425
36.3738-4.48753.02725.1852-2.72315.0232-0.3251-0.32220.0120.41970.29430.0591-0.1747-0.41760.03080.03570.01870.00280.03930.00550.0181-17.644318.912614.9214
40.53970.2029-0.02130.79090.15541.3458-0.0110.0165-0.0279-0.02470.0068-0.04040.06470.06910.00410.01470.005-0.00720.0173-0.00310.0529-9.585911.14760.7372
51.7164-1.54610.21793.4344-1.18292.1715-0.0040.0273-0.21780.01140.07760.28530.2806-0.1494-0.07370.074-0.02430.00090.0226-0.01490.0605-21.13940.4339-4.2157
67.47614.32632.18853.4972.71776.9511-0.1037-0.16670.54010.22-0.1930.4964-0.0052-0.62520.29670.11730.00520.04960.11320.0210.1026-22.9935-0.409739.2333
71.29930.1705-0.46761.5914-0.55683.06550.0553-0.0599-0.31740.1205-0.1261-0.05650.1956-0.12020.07090.122-0.0378-0.03570.02670.02880.1116-12.6959-8.350130.8121
81.84390.12960.55923.3995-0.03612.4394-0.04780.0172-0.3094-0.2376-0.078-0.07570.3293-0.0350.12570.29060.05080.02430.0155-0.01810.1903-5.3458-19.580312.0949
94.2533-2.1663-1.76941.82891.79024.2671-0.183-0.1689-0.62020.17880.0061-0.02060.68520.2640.17690.20840.0739-0.01280.05790.08930.34532.1471-16.052529.4671
101.04630.40350.00061.6412-0.38222.35930.03660.0449-0.2003-0.0302-0.0389-0.01390.2495-0.25540.00230.1182-0.0295-0.02790.04910.01520.1055-15.4459-6.626625.2033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 48
2X-RAY DIFFRACTION2A49 - 83
3X-RAY DIFFRACTION3A84 - 107
4X-RAY DIFFRACTION4A108 - 215
5X-RAY DIFFRACTION5A216 - 265
6X-RAY DIFFRACTION6B19 - 30
7X-RAY DIFFRACTION7B31 - 83
8X-RAY DIFFRACTION8B84 - 124
9X-RAY DIFFRACTION9B125 - 160
10X-RAY DIFFRACTION10B161 - 265

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