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- PDB-5uje: SbnI with C-terminal truncation from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 5uje
TitleSbnI with C-terminal truncation from Staphylococcus aureus
ComponentsSbnI protein
KeywordsGENE REGULATION / staphyloferrin B / heme / regulator / siderophore
Function / homology
Function and homology information


L-serine kinase (ATP) / positive regulation of sporulation resulting in formation of a cellular spore / phosphotransferase activity, alcohol group as acceptor / siderophore biosynthetic process / chromosome segregation / chromosome / kinase activity / DNA binding / ATP binding
Similarity search - Function
L-serine kinase SbnI-like / SbnI-like, N-terminal / L-serine kinase SerK/SbnI, C-terminal / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily
Similarity search - Domain/homology
SbnI protein / L-serine kinase SbnI
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMurphy, M.E.P. / Verstraete, M.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-49597 Canada
CitationJournal: J.Biol.Chem. / Year: 2018
Title: SbnI is a free serine kinase that generates O -phospho-l-serine for staphyloferrin B biosynthesis in Staphylococcus aureus .
Authors: Verstraete, M.M. / Perez-Borrajero, C. / Brown, K.L. / Heinrichs, D.E. / Murphy, M.E.P.
History
DepositionJan 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SbnI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3852
Polymers28,2931
Non-polymers921
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.120, 55.120, 92.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein SbnI protein


Mass: 28292.514 Da / Num. of mol.: 1 / Fragment: UNP residues 1-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Newman / Gene: sbnI, NWMN_0068 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KDC0, UniProt: Q2G1M5*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.18 M HEPES (pH 7.5), 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.959 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959 Å / Relative weight: 1
ReflectionResolution: 2.5→42.438 Å / Num. obs: 21681 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 2.922 % / Biso Wilson estimate: 55.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.062 / Χ2: 0.933 / Net I/σ(I): 15.77 / Num. measured all: 63331 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.572.9121.0071.814554156415640.6511.243100
2.57-2.642.9170.812.194621158615840.6940.99999.9
2.64-2.712.9080.612.794435152615250.7950.75399.9
2.71-2.82.9210.5143.234352149014900.8420.634100
2.8-2.892.9290.3574.14294146814660.9040.44199.9
2.89-2.992.940.2355.854060138213810.9590.2999.9
2.99-3.12.9340.2016.993905133613310.9610.24799.6
3.1-3.232.9360.1219.853811129812980.9860.15100
3.23-3.372.940.09312.373610122812280.9920.114100
3.37-3.542.9280.06616.133399116211610.9950.08199.9
3.54-3.732.9280.05220.683341114211410.9960.06499.9
3.73-3.952.930.04124.193150107610750.9970.0599.9
3.95-4.232.9490.03130.492952100210010.9980.03899.9
4.23-4.562.9170.02933.8926699209150.9980.03699.5
4.56-52.9220.02237.8825018568560.9990.027100
5-5.592.9280.02436.7822787867780.9990.0399
5.59-6.462.8820.02237.1918506526420.9980.02898.5
6.46-7.912.8870.02140.2616926025860.9990.02797.3
7.91-11.182.8470.01654.212444444370.9990.0298.4
11.18-42.4382.8380.02360.056132362160.9980.02891.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXphenix.refine: 1.8.2_1309refinement
XSCALEdata scaling
SOLVEphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→42.438 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 36.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 1086 5.01 %
Rwork0.2521 20595 -
obs0.2532 21681 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 532.65 Å2 / Biso mean: 115.4611 Å2 / Biso min: 37.62 Å2
Refinement stepCycle: final / Resolution: 2.5→42.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 14 12 1989
Biso mean--98.95 61.52 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032020
X-RAY DIFFRACTIONf_angle_d0.7252740
X-RAY DIFFRACTIONf_chiral_restr0.027299
X-RAY DIFFRACTIONf_plane_restr0.003348
X-RAY DIFFRACTIONf_dihedral_angle_d14.579747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5004-2.61410.42861380.385925992737100
2.6141-2.75190.43761360.37625682704100
2.7519-2.92430.40651360.360225902726100
2.9243-3.150.34721340.318325342668100
3.15-3.46690.291360.306326052741100
3.4669-3.96820.25011380.248825972735100
3.9682-4.99830.25961360.195925762712100
4.9983-42.44420.19971320.20282526265898
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)
12.76281.07481.5994.19430.17888.82590.05870.28340.0152-0.17710.0830.09640.4812-0.0762-0.07210.29880.10190.06430.49640.01460.25176.15049.538339.1347
25.0251-1.4316-0.02774.1143-2.43792.90950.6030.5003-0.0437-1.0077-0.6481-0.22290.15021.00090.20880.87430.02760.00230.7203-0.0290.3544-0.079323.457214.2727
30.48970.69540.43890.719-2.8668.7042-0.0333-0.06210.0117-0.08350.03180.04690.2723-0.0097-0.01890.54110.09640.01620.66680.0250.37892.743614.86436.1378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )A1 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 161 )A80 - 161
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 240 )A162 - 240

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