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- PDB-7l5r: Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-s... -

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Basic information

Entry
Database: PDB / ID: 7l5r
TitleCrystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase OXA-14 from Pseudomonas aeruginosa
Components(Beta-lactamase) x 2
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / class D beta-lactamase / OXA-14
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMinasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Brunzelle, J.S. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Antimicrob.Agents Chemother. / Year: 2022
Title: Functional and Structural Characterization of OXA-935, a Novel OXA-10-Family beta-Lactamase from Pseudomonas aeruginosa.
Authors: Pincus, N.B. / Rosas-Lemus, M. / Gatesy, S.W.M. / Bertucci, H.K. / Brunzelle, J.S. / Minasov, G. / Shuvalova, L.A. / Lebrun-Corbin, M. / Satchell, K.J.F. / Ozer, E.A. / Hauser, A.R. / Bachta, K.E.R.
History
DepositionDec 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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)58,00027
Polymers55,6102
Non-polymers2,39025
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-243 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.813, 96.346, 125.137
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.: 1
Source method: isolated from a genetically manipulated source
Details: The side chain of Lys-70 is N-carboxylated / 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: Protein Beta-lactamase / OXA-14 Beta-lactamase


Mass: 27783.510 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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 / pH: 9
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; Cryo: 2M Lithium sulfate

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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: 1.65→30 Å / Num. obs: 71761 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.027 / Rrim(I) all: 0.066 / Rsym value: 0.06 / Χ2: 1.007 / Net I/σ(I): 27
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3530 / CC1/2: 0.8 / CC star: 0.943 / Rpim(I) all: 0.365 / Rrim(I) all: 0.919 / Rsym value: 0.841 / Χ2: 1.001 / % 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: 1.65→29.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.517 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3543 4.9 %RANDOM
Rwork0.1636 ---
obs0.1648 68142 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.72 Å2 / Biso mean: 25.851 Å2 / Biso min: 12.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--1.2 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: final / Resolution: 1.65→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 128 505 4444
Biso mean--54.39 36.45 -
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173729
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.6295582
X-RAY DIFFRACTIONr_angle_other_deg0.3511.5748712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1235506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49424.242198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.22615725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8551515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0570.024508
X-RAY DIFFRACTIONr_gen_planes_other0.0530.02813
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 237 -
Rwork0.245 4889 -
all-5126 -
obs--97.56 %
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)
14.7361-0.5336-2.17422.85780.48031.979-0.12340.0367-0.4928-0.1709-0.0760.37390.176-0.08910.19940.1364-0.0591-0.01880.1409-0.04270.1028-21.5902-3.4884-15.0693
20.51960.20020.51131.1780.73732.2056-0.05680.0828-0.0466-0.06530.0541-0.06040.05710.09430.00260.0247-0.01590.02120.0743-0.01130.0313-11.05926.2459-5.484
35.5175-3.65832.84263.8666-2.09543.4516-0.2685-0.28680.03650.34330.22840.0121-0.2316-0.25020.04010.03620.01920.0010.09650.00020.0017-17.52819.374615.0462
40.64790.1886-0.1710.57580.04781.2489-0.0418-0.0142-0.0334-0.0490.0516-0.06380.02330.0343-0.00980.0106-0.00720.00030.07060.00010.0254-8.217711.1291.5379
52.3663-2.07081.10023.3113-1.15272.0532-0.04170.0014-0.0850.00120.00770.06810.1172-0.11680.0340.029-0.03520.0120.0639-0.0130.0162-18.44833.9851-4.3039
61.6795-2.44470.63637.5941-1.72421.28210.0015-0.0445-0.16330.06250.05890.31070.1023-0.2242-0.06040.0304-0.04490.01010.0726-0.01050.0365-26.13580.7821-4.2609
71.03710.48670.18612.7334-0.24613.10970.0834-0.1397-0.03970.1787-0.11790.1486-0.0415-0.47160.03450.0511-0.0435-0.00080.19010.03350.0333-19.8231-5.146836.3704
82.29670.1820.6782.8531-0.66683.4981-0.0320.1911-0.2941-0.481-0.1664-0.30540.47930.31680.19850.13330.06570.09940.06560.03230.1475-1.2203-12.265713.8527
95.7483-1.94911.88353.2377-1.50154.62450.14670.2207-0.6299-0.4219-0.0160.03950.68590.1477-0.13070.15580.04530.06210.0570.03690.1741-0.3212-18.317219.6029
101.28550.1985-0.67071.8746-0.94793.0764-0.0697-0.0917-0.2023-0.002-0.1651-0.3560.19170.22040.23480.01870.0014-0.00510.08570.07520.1327-2.5245-8.333127.7784
110.62060.44870.0151.962-1.2522.85080.002-0.0008-0.0982-0.096-0.0320.0030.232-0.36630.030.0529-0.0419-0.00210.15970.02970.0569-18.0609-8.097325.589
121.6107-1.25021.017310.0652-2.19121.95650.057-0.0447-0.0532-0.36670.14660.35350.2396-0.4128-0.20360.0367-0.0635-0.02780.18530.04380.03-25.8148-9.04126.0412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 38
2X-RAY DIFFRACTION2A39 - 83
3X-RAY DIFFRACTION3A84 - 107
4X-RAY DIFFRACTION4A108 - 203
5X-RAY DIFFRACTION5A204 - 240
6X-RAY DIFFRACTION6A241 - 265
7X-RAY DIFFRACTION7B19 - 68
8X-RAY DIFFRACTION8B69 - 111
9X-RAY DIFFRACTION9B112 - 131
10X-RAY DIFFRACTION10B132 - 192
11X-RAY DIFFRACTION11B193 - 243
12X-RAY DIFFRACTION12B244 - 265

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