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- PDB-6rtn: Crystal structure of OXA-10 with VNRX-5133 -

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Basic information

Entry
Database: PDB / ID: 6rtn
TitleCrystal structure of OXA-10 with VNRX-5133
ComponentsBeta-lactamase OXA-10
KeywordsANTIMICROBIAL PROTEIN / beta lactamase / antibiotic resistance / boronates
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KJK / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsBrem, J. / Schofield, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: J.Med.Chem. / Year: 2019
Title: Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-beta-Lactamases.
Authors: Krajnc, A. / Brem, J. / Hinchliffe, P. / Calvopina, K. / Panduwawala, T.D. / Lang, P.A. / Kamps, J.J.A.G. / Tyrrell, J.M. / Widlake, E. / Saward, B.G. / Walsh, T.R. / Spencer, J. / Schofield, C.J.
History
DepositionMay 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 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

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)56,60116
Polymers55,3972
Non-polymers1,20414
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-130 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.879, 95.620, 126.269
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: 27698.490 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-KJK / (3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid


Mass: 389.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28BN3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M MES, pH = 6.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97872 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 18, 2018 / Details: mirror
RadiationMonochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.17→76.25 Å / Num. obs: 32199 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.073 / Rrim(I) all: 0.259 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.17-2.2312.60.823540.8830.2610.931100
9.7-76.2510.30.14290.9970.0320.10699.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.28 Å76.23 Å
Translation4.28 Å76.23 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQ9

5fq9


Resolution: 2.17→63.134 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.64
RfactorNum. reflection% reflection
Rfree0.2236 1614 5.02 %
Rwork0.1948 --
obs0.1962 32125 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.74 Å2 / Biso mean: 22.4515 Å2 / Biso min: 3.07 Å2
Refinement stepCycle: final / Resolution: 2.17→63.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 68 304 4130
Biso mean--25.49 28.59 -
Num. residues----491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1691-2.23290.23891270.22092486261399
2.2329-2.3050.30431250.24624952620100
2.305-2.38730.23361220.209125222644100
2.3873-2.48290.24261030.20925262629100
2.4829-2.59590.20251340.202525282662100
2.5959-2.73280.22671470.200825122659100
2.7328-2.9040.24871360.206225272663100
2.904-3.12820.25641540.201724922646100
3.1282-3.4430.20631280.183225612689100
3.443-3.94120.211390.165825492688100
3.9412-4.96520.15721450.148325952740100
4.9652-63.16120.2561540.228527182872100
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)
16.873-3.2685-1.43374.49070.41774.17920.10810.42030.9734-0.3299-0.321-0.7598-0.59110.56330.04530.3091-0.04890.04830.24170.08670.306822.05734.5198-15.4682
20.81930.4888-0.57382.1778-0.66052.7524-0.01680.02340.06240.00630.00610.0528-0.0599-0.03770.03380.06320.0361-0.02320.143-0.01840.145911.954-7.3586-2.8715
35.6379-3.41240.7182.6494-1.76256.0369-0.1571-0.0183-0.02770.41430.16-0.2793-0.18420.2801-0.03770.16690.0122-0.00220.1528-0.04060.152519.3304-17.718212.4067
43.46410.58322.24173.1724-1.51025.00660.0355-0.1562-0.08990.09460.12590.06230.2071-0.1652-0.14970.1030.01270.02070.0709-0.02670.1054.8276-20.24012.4356
52.4320.69010.79573.9122-1.55785.14630.02670.1009-0.2887-0.3087-0.0195-0.00170.38470.31340.01030.1598-0.00330.0130.1702-0.00450.10719.283-18.5213-6.7337
62.1035-0.8363-0.87521.83660.07942.551-0.0495-0.1010.10090.12710.06750.0655-0.2232-0.0677-0.0020.17890.0199-0.02060.11960.01130.13188.8151-1.71673.0913
74.1339-1.8021-0.4365.66441.03912.9322-0.05130.14290.1321-0.02510.0103-0.344-0.05340.0489-0.0040.1022-0.0255-0.02220.13340.03930.057719.0578-4.1586-5.7827
86.0926-5.0760.96474.4379-1.08933.40520.09050.0690.14830.1869-0.1917-0.5651-0.29810.06310.08690.1606-0.0518-0.00420.1885-0.01510.196825.44961.8151-4.2857
91.3896-0.07140.87511.3857-0.00292.98020.0193-0.0520.09810.0646-0.0382-0.0752-0.01880.26020.00670.1115-0.01650.02730.1581-0.02350.132813.23598.011730.0973
105.48921.78071.32292.1121-2.21667.74690.0730.2910.19-0.3079-0.1941-0.2024-0.24290.14650.05520.24940.0343-0.00180.19470.01240.17597.78121.05511.773
113.8178-0.2346-0.50782.0233-2.03874.64790.04970.1650.173-0.08950.11550.3941-0.2642-0.3593-0.1090.13960.0261-0.01170.1602-0.03970.1906-4.172215.203124.2809
123.6446-1.28140.8151.3265-0.31393.4786-0.2248-0.27680.29020.22220.27930.2776-0.6381-0.25690.07390.21280.01970.02520.1855-0.05950.24711.77317.599932.6212
134.24490.22242.39493.01851.32474.56630.2033-0.1597-0.21630.2018-0.11270.30070.3525-0.1508-0.13070.1178-0.01440.01360.12690.00770.12615.19910.906127.9737
142.96180.4056-0.06752.6564-0.12082.42030.06270.26690.0351-0.3064-0.00550.02710.20430.2449-0.02910.20630.0393-0.00220.1439-0.00560.101511.62093.909817.6025
153.16521.30070.29247.13821.03792.93750.00720.01120.20750.13720.0716-0.1775-0.10840.19040.02490.0778-0.00810.01960.17630.03950.119717.377910.252928.9732
164.5595-1.4445-0.85599.51740.9543.256-0.15530.31240.0476-0.11430.2314-0.76140.04350.3212-0.02150.1023-0.0030.02640.30680.00670.164525.32348.561426.4148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 35 )A20 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 89 )A36 - 89
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 116 )A90 - 116
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 138 )A117 - 138
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 162 )A139 - 162
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 208 )A163 - 208
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 243 )A209 - 243
8X-RAY DIFFRACTION8chain 'A' and (resid 244 through 264 )A244 - 264
9X-RAY DIFFRACTION9chain 'B' and (resid 19 through 89 )B19 - 89
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 116 )B90 - 116
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 139 )B117 - 139
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 162 )B140 - 162
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 181 )B163 - 181
14X-RAY DIFFRACTION14chain 'B' and (resid 182 through 208 )B182 - 208
15X-RAY DIFFRACTION15chain 'B' and (resid 209 through 243 )B209 - 243
16X-RAY DIFFRACTION16chain 'B' and (resid 244 through 264 )B244 - 264

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