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- PDB-6o9w: Crystal structure of Staphylococcus aureus BlaR1 antibiotic-senso... -

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Basic information

Entry
Database: PDB / ID: 6o9w
TitleCrystal structure of Staphylococcus aureus BlaR1 antibiotic-sensor domain in complex with avibactam
ComponentsRegulatory protein BlaR1
KeywordsSIGNALING PROTEIN / beta-lactam antibiotic sensor domain / Antibiotic complex / penicillin binding protein
Function / homology
Function and homology information


penicillin binding / cell wall organization / plasma membrane
Similarity search - Function
Peptidase M56 / BlaR1 peptidase M56 / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / Regulatory protein BlaR1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 15, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein BlaR1
B: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3654
Polymers60,8312
Non-polymers5352
Water3,009167
1
A: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6832
Polymers30,4151
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6832
Polymers30,4151
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.355, 92.647, 56.472
Angle α, β, γ (deg.)90.000, 104.570, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 337 through 583)
21(chain B and (resid 337 through 407 or resid 428 through 583))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRASNASN(chain A and resid 337 through 583)AA337 - 58311 - 257
21TYRTYRASPASP(chain B and (resid 337 through 407 or resid 428 through 583))BB337 - 40711 - 81
22GLNGLNASNASN(chain B and (resid 337 through 407 or resid 428 through 583))BB428 - 583102 - 257

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Components

#1: Protein Regulatory protein BlaR1


Mass: 30415.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18357
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 200 mM tri-potassium citrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→46.32 Å / Num. obs: 38646 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.061 / Rrim(I) all: 0.114 / Net I/σ(I): 6.7 / Num. measured all: 131091 / Scaling rejects: 1
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.984 / Num. measured all: 9292 / Num. unique obs: 2689 / CC1/2: 0.61 / Rpim(I) all: 0.618 / Rrim(I) all: 1.165 / Net I/σ(I) obs: 0.9 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.61 Å46.32 Å
Translation4.61 Å46.32 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XA1

1xa1


Resolution: 1.95→46.32 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.97
RfactorNum. reflection% reflection
Rfree0.2248 1823 4.72 %
Rwork0.1848 --
obs0.1867 38592 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.99 Å2 / Biso mean: 44.9278 Å2 / Biso min: 21.03 Å2
Refinement stepCycle: final / Resolution: 1.95→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 112 167 4195
Biso mean--35.33 41.28 -
Num. residues----472
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1358X-RAY DIFFRACTION5.016TORSIONAL
12B1358X-RAY DIFFRACTION5.016TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.00270.38561340.32232793292799
2.0027-2.06170.32051520.29128022954100
2.0617-2.12820.29371440.2622816296099
2.1282-2.20430.26671470.237628142961100
2.2043-2.29250.27881420.22662809295199
2.2925-2.39690.22021500.204828232973100
2.3969-2.52320.23771470.192728142961100
2.5232-2.68130.19851340.179228492983100
2.6813-2.88830.20591360.170328332969100
2.8883-3.17890.21951430.172428372980100
3.1789-3.63870.20641410.162819296099
3.6387-4.58380.17881270.144128632990100
4.5838-46.33660.221260.17692897302399
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)
13.9418-0.7081.74193.1373-0.6784.1687-0.1355-0.18890.50150.18890.00720.0628-0.2686-0.19150.17980.30710.0097-0.02340.1863-0.02220.3246-5.5467-6.261624.3123
23.6413-1.09440.10394.4830.15232.04860.3208-0.114-0.2157-0.1724-0.2030.24180.255-0.0825-0.10340.2678-0.0372-0.04460.2101-0.00760.2166-8.8569-25.381526.7838
38.16044.8607-2.78548.1541.46142.8241-0.41030.1512-0.4982-0.47330.3863-0.20240.09870.21170.00420.41520.0837-0.05480.2993-0.05750.3252-3.2441-35.840917.5654
41.420.30160.0731.03060.09121.2960.0466-0.0287-0.03980.03920.00340.05650.1151-0.0722-0.04440.29340.0005-0.05840.2252-0.00990.2736-6.1806-23.178323.454
52.12522.54142.10158.83852.05998.03690.10060.3438-0.1226-0.61580.1579-0.8099-0.10390.5307-0.23630.254-0.04510.04310.29770.00640.34262.7892-9.073512.079
63.2986-0.60825.0396.3891-0.73247.6710.43081.216-1.0605-0.6177-0.36470.43870.5120.1215-0.13870.53020.1155-0.02670.4544-0.13950.4563-26.9671-46.6829-7.9664
72.06450.42830.94581.601-1.55833.40820.0010.1988-0.1356-0.1066-0.03410.00910.00250.07320.02370.26020.0249-0.01990.2056-0.05150.2578-29.986-37.15690.373
83.08332.221-1.78721.5855-1.37981.18740.1581-0.6320.0475-0.5588-0.59340.19040.1073-0.03160.37350.88950.0177-0.09351.0493-0.1710.813-34.804-30.638430.2887
92.088-0.72571.01471.8267-0.00612.74170.0934-0.1834-0.11870.1251-0.03120.06490.1317-0.1284-0.07150.2379-0.035-0.02520.21730.0070.2596-30.7638-40.356912.4523
105.22111.78230.95383.04781.04851.9084-0.0670.06410.0582-0.0765-0.070.1751-0.2028-0.01450.17090.28020.0196-0.04680.2113-0.02010.2488-30.9551-28.84991.3527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 337:379)A337 - 379
2X-RAY DIFFRACTION2(chain A and resid 380:404)A380 - 404
3X-RAY DIFFRACTION3(chain A and resid 405:439)A405 - 439
4X-RAY DIFFRACTION4(chain A and resid 440:572)A440 - 572
5X-RAY DIFFRACTION5(chain A and resid 573:583)A573 - 583
6X-RAY DIFFRACTION6(chain B and resid 337:347)B337 - 347
7X-RAY DIFFRACTION7(chain B and resid 348:405)B348 - 405
8X-RAY DIFFRACTION8(chain B and resid 406:427)B406 - 427
9X-RAY DIFFRACTION9(chain B and resid 428:525)B428 - 525
10X-RAY DIFFRACTION10(chain B and resid 526:583)B526 - 583

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