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- PDB-7b3u: OXA-10 beta-lactamase with covalent modification -

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Basic information

Entry
Database: PDB / ID: 7b3u
TitleOXA-10 beta-lactamase with covalent modification
ComponentsBeta-lactamase OXA-10
KeywordsHYDROLASE / beta lactamase / antibiotic resistance / tazobactam / dehydroalanine / irreversible inhibition / covalent modification
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/transpeptidase-like
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.598 Å
AuthorsLang, P.A. / Brem, J. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MRF-145-0004-TPG-AVISO United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Studies on enmetazobactam clarify mechanisms of widely used beta-lactamase inhibitors.
Authors: Lang, P.A. / Raj, R. / Tumber, A. / Lohans, C.T. / Rabe, P. / Robinson, C.V. / Brem, J. / Schofield, C.J.
History
DepositionDec 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase OXA-10
B: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,16011
Polymers55,4312
Non-polymers7289
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-94 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.935, 97.222, 125.988
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-10 / Beta-lactamase PSE-2


Mass: 27715.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14489, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium sulfate, 0.1 M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96856 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96856 Å / Relative weight: 1
ReflectionResolution: 1.598→77.02 Å / Num. obs: 80334 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.044 / Rrim(I) all: 0.158 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.6411.81.2756935758740.8160.3851.3331.7100
7.16-77.0211.70.061218110390.9980.0180.06321.499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.22 Å48.74 Å
Translation4.22 Å48.74 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K55

1k55


Resolution: 1.598→52.867 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1767 4113 5.13 %
Rwork0.1551 76113 -
obs0.1563 80226 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.23 Å2 / Biso mean: 27.5105 Å2 / Biso min: 10.32 Å2
Refinement stepCycle: final / Resolution: 1.598→52.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 49 576 4435
Biso mean--35.59 37.48 -
Num. residues----493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5983-1.61710.27431290.2347245995
1.6171-1.63680.22861480.20912594100
1.6368-1.65760.2531450.20022574100
1.6576-1.67940.22821330.18382639100
1.6794-1.70240.20541410.18632579100
1.7024-1.72670.19441370.18552596100
1.7267-1.75250.21421620.18232590100
1.7525-1.77990.22911290.18282568100
1.7799-1.8090.23061420.19612637100
1.809-1.84020.2151340.18282591100
1.8402-1.87370.19781540.17482609100
1.8737-1.90970.20571270.18042597100
1.9097-1.94870.18221470.15972613100
1.9487-1.99110.18421300.15652602100
1.9911-2.03740.17391000.15842680100
2.0374-2.08840.18491330.14952590100
2.0884-2.14480.19461540.14932632100
2.1448-2.2080.18331270.14922621100
2.208-2.27920.16361390.14672625100
2.2792-2.36070.1751540.14932597100
2.3607-2.45520.18181340.14682668100
2.4552-2.56690.17971350.15362642100
2.5669-2.70230.17371600.15392631100
2.7023-2.87160.18311590.15232636100
2.8716-3.09330.16941500.15292632100
3.0933-3.40450.16881540.14592656100
3.4045-3.8970.15361590.14272674100
3.897-4.90920.12081540.1182723100
4.9092-52.8670.20171430.17642858100
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)
13.8504-2.8581-2.07473.92951.68033.868-0.10410.5448-0.7976-0.1522-0.38870.86130.3881-0.56530.45780.3419-0.0371-0.07190.2482-0.12350.3607-21.4851-3.7353-16.0984
29.6464-4.55964.95496.3365-3.12167.9854-0.03870.3033-0.1693-0.0637-0.09360.02250.45240.41680.1190.1917-0.00720.01080.1251-0.03890.1153-14.9234-2.09-12.3804
31.131.65311.76978.18767.48469.0015-0.10960.1271-0.0418-0.33940.11790.0345-0.33230.14720.01040.0738-0.0057-0.00390.11270.0160.1141-14.715610.7745-11.1299
44.83951.2692-3.06811.38020.67044.2984-0.1277-0.20610.00470.13260.0196-0.05520.08880.38740.11130.12020.0437-0.01930.10120.00830.139-5.386713.84899.9659
56.9218-6.38110.58398.46260.57855.2715-0.1979-0.2029-0.05420.09550.2260.25820.0016-0.392-0.01820.0933-0.01420.01490.14630.03810.1083-19.833917.844312.4529
61.03340.1545-0.04921.67250.28471.4021-0.02420.0159-0.01470.03720.0441-0.0170.11710.0755-0.01770.09420.0163-0.00150.110.00370.0987-7.938911.4833-0.1946
73.9214-2.56740.07135.6082-0.241.9882-0.05980.0028-0.2515-0.02350.04030.38560.2096-0.1571-0.02580.1264-0.02820.02260.1169-0.01430.1095-22.02884.2017-6.5329
83.31313.43510.89188.39251.37012.55510.1708-0.14330.14030.3118-0.17970.5257-0.1444-0.54120.0120.14650.03460.03380.28670.02970.1823-23.2051-5.139635.3568
92.1563-0.7654-2.26811.73860.66754.36780.0542-0.0471-0.0992-0.0885-0.1296-0.0915-0.02120.0620.08530.0996-0.0065-0.0430.13640.020.1499-7.4804-8.811526.249
105.7954-0.8874-1.5085.15814.11976.227-0.06730.1156-0.6914-0.2231-0.06280.2530.9136-0.57170.1070.466-0.00820.01940.2318-0.00170.2898-8.0515-21.125510.0844
111.6532-0.6386-0.20721.8917-0.30532.3030.0084-0.0031-0.1368-0.0564-0.0225-0.18190.13320.17210.01280.10420.0066-00.12080.02420.1651-1.9441-10.874625.0108
123.2667-0.58150.44224.16830.26893.63360.03570.0774-0.2376-0.1365-0.13790.1075-0.0646-0.331-0.01330.09970.0207-0.00280.1594-0.00990.1125-16.7967-10.170724.4763
133.3481.3830.12615.3307-1.09622.5085-0.06940.153-0.0719-0.30170.20420.51980.0453-0.5492-0.11080.13620.0043-0.0240.27820.01480.1606-22.8241-7.898426.364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 35 )A19 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 55 )A36 - 55
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 69 )A56 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 89 )A70 - 89
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 116 )A90 - 116
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 208 )A117 - 208
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 264 )A209 - 264
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 45 )B19 - 45
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 89 )B46 - 89
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 116 )B90 - 116
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 196 )B117 - 196
12X-RAY DIFFRACTION12chain 'B' and (resid 197 through 228 )B197 - 228
13X-RAY DIFFRACTION13chain 'B' and (resid 229 through 265 )B229 - 265

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