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- PDB-6o9s: Crystal structure of Staphylococcus aureus MecR1 antibiotic-senso... -

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Basic information

Entry
Database: PDB / ID: 6o9s
TitleCrystal structure of Staphylococcus aureus MecR1 antibiotic-sensor domain in complex with avibactam
ComponentsMethicillin resistance mecR1 protein
KeywordsSIGNALING PROTEIN / beta-lactam antibiotic sensor domain / Antibiotic complex
Function / homology
Function and homology information


penicillin binding / response to antibiotic
Similarity search - Function
Peptidase M56 / BlaR1 peptidase M56 / 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-NXL / Methicillin resistance mecR1 protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsAlexander, J.A.N. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural analysis of avibactam-mediated activation of the bla and mec divergons in methicillin-resistant Staphylococcus aureus .
Authors: Alexander, J.A.N. / Radaeva, M. / King, D.T. / Chambers, H.F. / Cherkasov, A. / Chatterjee, S.S. / Strynadka, N.C.J.
History
DepositionMar 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: 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 11, 2023Group: 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: Methicillin resistance mecR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5923
Polymers30,2281
Non-polymers3632
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.672, 58.672, 147.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Methicillin resistance mecR1 protein


Mass: 30228.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mecR1, mecR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A0B1
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.5 M ammonium sulphate, 50 mM HEPES pH 7.5, 1 mM oxacillin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.984 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.59→45.93 Å / Num. obs: 35378 / % possible obs: 99.2 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Net I/σ(I): 20.5
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.526 / Num. unique obs: 1610 / CC1/2: 0.791 / Rpim(I) all: 0.275 / Rrim(I) all: 0.599 / % possible all: 91.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.4 Å45.93 Å
Translation6.4 Å45.93 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.15data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IWB

2iwb


Resolution: 1.59→45.927 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.77
RfactorNum. reflection% reflection
Rfree0.1967 1689 4.79 %
Rwork0.1576 --
obs0.1594 35297 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.87 Å2 / Biso mean: 30.9179 Å2 / Biso min: 11.95 Å2
Refinement stepCycle: final / Resolution: 1.59→45.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 33 159 2257
Biso mean--45.49 36.04 -
Num. residues----246
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 (%)
1.59-1.63680.26131220.21612561268392
1.6368-1.68960.21671360.19472710284699
1.6896-1.750.19041600.169327602920100
1.75-1.82010.18761350.162227782913100
1.8201-1.90290.17411320.148927962928100
1.9029-2.00330.17691360.14427732909100
2.0033-2.12880.16741390.145828162955100
2.1288-2.29310.1921520.141328022954100
2.2931-2.52390.21221340.147228482982100
2.5239-2.8890.19241330.158228482981100
2.889-3.63960.2071400.157729043044100
3.6396-45.9460.19981700.1633012318299
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)
17.34081.3389-1.15873.25910.87183.71560.2173-1.2496-0.41980.6447-0.08850.0570.03350.2168-0.05640.2787-0.02390.04340.25940.07220.139652.364976.84176.7434
24.665-0.5064-0.83083.54610.83473.4448-0.1764-0.0123-0.30520.09980.06190.03650.1199-0.16810.08570.2023-0.02450.03480.14850.03170.241547.516167.3025162.4527
31.88340.5141-0.33890.94480.03791.02130.034-0.12770.00070.1061-0.0095-0.0067-0.08560.0243-0.02210.15280.0030.00290.1126-0.00650.110157.603383.6291165.6622
45.2293-2.3863-1.93475.71792.95135.48860.31070.21920.0889-0.6361-0.0272-0.4954-0.38070.5357-0.22850.2298-0.0240.02350.27870.01140.192673.191889.4946145.565
53.714-1.6408-0.7473.82860.32712.52070.16340.4115-0.2102-0.3773-0.16030.1496-0.15690.1554-0.00210.21610.0154-0.01060.2226-0.01610.167167.75986.5118146.7285
67.08733.15144.48456.47612.47239.7316-0.03620.13480.02460.15760.2225-0.5469-0.34890.6301-0.15760.2407-0.05440.01050.2756-0.03440.215977.124489.9311158.7044
72.10080.5282-2.47116.573-0.42917.65020.0469-0.40790.23960.2822-0.0538-0.4095-0.21450.644-0.00040.2159-0.0754-0.02660.2268-0.04510.168671.807590.5696170.2121
85.8599-0.2998-0.59362.99250.4073.88860.1042-0.1252-0.07630.0739-0.0386-0.26250.03180.3992-0.06530.1648-0.0119-0.01450.13870.00350.12767.918780.1773166.5678
98.44110.24361.86636.80112.20834.7536-0.1868-0.33060.69990.16220.1020.5027-0.58290.18920.07150.2669-0.02650.0030.1599-0.03290.213357.5194.6186167.0996
104.65593.61332.67094.13334.5936.958-0.1147-0.11860.4462-0.0278-0.01450.2917-0.4593-0.0260.14920.2590.04070.01750.15550.02860.207957.326695.2107155.4913
114.6508-2.4591-4.26096.0112-0.81265.89590.1260.5960.5548-0.8176-0.21970.9903-0.8093-1.56250.10870.32480.1459-0.10980.5974-0.00740.290643.326791.2474150.7232
126.6633-5.97790.98988.0639-0.59712.7310.23080.2771-0.1781-0.0783-0.1961-0.10040.150.1221-0.01880.11750.00760.00770.1448-0.01340.132861.408374.4951155.5905
133.609-1.9622-0.77173.40321.03661.56740.1230.04370.1136-0.0024-0.1358-0.0113-0.1088-0.1290.02910.13750.00230.01680.1176-0.00290.128350.300683.3183161.1551
148.914-4.5275-0.02682.30760.15093.81910.24510.271-0.7105-0.2742-0.19050.30860.32730.0604-0.0630.18040.0025-0.0190.1462-0.01460.213154.91271.1272154.0507
152.3506-2.1861.45492.37320.17518.5317-0.2230.01690.1522-0.4397-0.37351.1697-0.2163-0.67910.49310.1997-0.0283-0.03630.2692-0.05320.396441.335278.9193156.6974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 340:350)A340 - 350
2X-RAY DIFFRACTION2(chain A and resid 351:363)A351 - 363
3X-RAY DIFFRACTION3(chain A and resid 364:407)A364 - 407
4X-RAY DIFFRACTION4(chain A and resid 408:423)A408 - 423
5X-RAY DIFFRACTION5(chain A and resid 424:444)A424 - 444
6X-RAY DIFFRACTION6(chain A and resid 445:452)A445 - 452
7X-RAY DIFFRACTION7(chain A and resid 453:463)A453 - 463
8X-RAY DIFFRACTION8(chain A and resid 464:491)A464 - 491
9X-RAY DIFFRACTION9(chain A and resid 492:504)A492 - 504
10X-RAY DIFFRACTION10(chain A and resid 505:517)A505 - 517
11X-RAY DIFFRACTION11(chain A and resid 518:523)A518 - 523
12X-RAY DIFFRACTION12(chain A and resid 524:541)A524 - 541
13X-RAY DIFFRACTION13(chain A and resid 542:562)A542 - 562
14X-RAY DIFFRACTION14(chain A and resid 563:576)A563 - 576
15X-RAY DIFFRACTION15(chain A and resid 577:585)A577 - 585

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