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- PDB-6uex: Crystal structure of S. aureus LcpA in complex with octaprenyl-py... -

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Basic information

Entry
Database: PDB / ID: 6uex
TitleCrystal structure of S. aureus LcpA in complex with octaprenyl-pyrophosphate-GlcNAc
ComponentsRegulatory protein MsrR
KeywordsTRANSFERASE / LytR / CpsA / Psr
Function / homology: / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / plasma membrane / Chem-Q5S / Regulatory protein MsrR
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, F.K.K. / Strynadka, N.C.J.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystallographic analysis ofStaphylococcus aureusLcpA, the primary wall teichoic acid ligase.
Authors: Li, F.K.K. / Rosell, F.I. / Gale, R.T. / Simorre, J.P. / Brown, E.D. / Strynadka, N.C.J.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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

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Assembly

Deposited unit
A: Regulatory protein MsrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,43011
Polymers30,6471
Non-polymers1,78310
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Regulatory protein MsrR
hetero molecules

A: Regulatory protein MsrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,86022
Polymers61,2942
Non-polymers3,56520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5290 Å2
ΔGint-189 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.245, 90.543, 94.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

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Components

#1: Protein Regulatory protein MsrR


Mass: 30647.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: msrR, SA1195 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99Q02
#2: Chemical ChemComp-Q5S / 2-(acetylamino)-2-deoxy-1-O-[(S)-hydroxy{[(S)-hydroxy{[(2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]oxy}phosphoryl]oxy}phosphoryl]-alpha-D-glucopyranose


Mass: 926.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H81NO12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.46 Å3/Da / Density % sol: 64.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 2.4 M ammonium sulfate, 0.08 M citric acid pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→47.38 Å / Num. obs: 30587 / % possible obs: 99.84 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04999 / Net I/σ(I): 16.31
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 1.514 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 3021 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXH

3nxh


Resolution: 1.9→47.377 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.55
RfactorNum. reflection% reflection
Rfree0.2258 1528 5 %
Rwork0.1922 --
obs0.1939 30547 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.25 Å2 / Biso mean: 67.3216 Å2 / Biso min: 33.6 Å2
Refinement stepCycle: final / Resolution: 1.9→47.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 110 57 2063
Biso mean--91.91 64.62 -
Num. residues----247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9001-1.96140.36071370.33392601
1.9614-2.03150.30531360.29032593
2.0315-2.11280.27371380.25122636
2.1128-2.2090.28051370.23862594
2.209-2.32550.23741370.20772612
2.3255-2.47110.26741380.20912616
2.4711-2.66190.24141390.20292640
2.6619-2.92980.21681390.19582622
2.9298-3.35360.23551400.19882654
3.3536-4.22480.21561400.17582678
4.2248-47.3770.2061470.17712773
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)
13.3959-0.218-0.69758.06065.9156.92470.0113-0.1618-0.3174-0.3243-0.26140.6286-0.31110.12850.23940.35930.0025-0.01030.35510.01740.450760.824312.161253.0581
28.4845-3.5391-2.52648.30991.34874.07240.3876-0.23550.16150.3777-0.1891-0.2319-0.30230.0337-0.3160.3385-0.1209-0.04760.3283-0.03470.473468.027717.239155.8625
35.80611.6727-1.48835.59032.78526.61210.1336-0.2246-0.77390.4384-0.1297-0.64890.44930.14890.02260.4031-0.0009-0.03570.30760.03670.548571.16317.544353.3853
47.0213-4.32281.85444.2102-2.62482.33960.009-0.3527-0.67240.11230.21320.9098-0.1774-0.5037-0.27560.39190.0180.01630.37570.01870.56151.354216.009752.3369
58.9864-0.2584-2.87177.21170.17017.67760.20251.88720.064-0.9776-0.06260.4905-0.1897-0.2732-0.16620.57660.1264-0.09510.59480.06260.47652.47522.622737.7556
62.5426-1.5292-2.43964.6025-0.86283.9840.2414-0.1370.2180.191-0.1933-0.0567-0.5230.5240.02260.50650.0201-0.040.39960.00620.614156.97324.536448.3539
76.92751.0042-2.50141.93290.92127.29960.50450.15210.3068-0.1022-0.23710.6091-0.4887-1.2725-0.23950.5943-0.00190.18640.81630.06830.760546.911815.370261.9278
89.7773-0.1891-6.11834.0916-1.318.45780.3625-0.08971.03620.45190.12520.1316-0.5421-0.597-0.4260.4465-0.0784-0.01660.5426-0.10320.375162.627523.18457.3015
96.46040.57780.31028.0329-2.34983.5948-0.0299-0.52660.08160.24690.1206-0.5689-0.04481.0827-0.43650.4224-0.14620.00060.43410.01110.565176.02619.910652.479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 81 through 109 )A81 - 109
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 131 )A110 - 131
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 156 )A132 - 156
4X-RAY DIFFRACTION4chain 'A' and (resid 157 through 187 )A157 - 187
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 222 )A188 - 222
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 242 )A223 - 242
7X-RAY DIFFRACTION7chain 'A' and (resid 243 through 267 )A243 - 267
8X-RAY DIFFRACTION8chain 'A' and (resid 268 through 301 )A268 - 301
9X-RAY DIFFRACTION9chain 'A' and (resid 302 through 327 )A302 - 327

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