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- PDB-7spq: Crystal structure of Burkholderia glumae toxoflavin biosynthesis ... -

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Basic information

Entry
Database: PDB / ID: 7spq
TitleCrystal structure of Burkholderia glumae toxoflavin biosynthesis protein ToxD
ComponentsSerine/threonine kinase ToxD
KeywordsUNKNOWN FUNCTION / Toxoflavin / biosynthesis protein
Function / homologySulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / kinase activity / phosphorylation / CITRIC ACID / Serine/threonine kinase
Function and homology information
Biological speciesBurkholderia glumae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFenwick, M.K. / Philmus, B. / Ealick, S.E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK067081 United States
Robert A. Welch FoundationA0034 United States
CitationJournal: To Be Published
Title: Crystal structure of Burkholderia glumae toxoflavin biosynthesis protein ToxD
Authors: Fenwick, M.K. / Begley, T.P. / Ealick, S.E. / Philmus, B.
History
DepositionNov 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine kinase ToxD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7927
Polymers35,7411
Non-polymers1,0516
Water8,467470
1
A: Serine/threonine kinase ToxD
hetero molecules

A: Serine/threonine kinase ToxD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,58414
Polymers71,4822
Non-polymers2,10212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area7210 Å2
ΔGint-44 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.978, 135.978, 135.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine kinase ToxD


Mass: 35741.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia glumae (bacteria) / Strain: BGR1 / Gene: bglu_2g06430 / Plasmid: pTHT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5AMM8

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Non-polymers , 5 types, 476 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Emerald BioSystems Wizard 1, formulation 6 [20% (w/v) PEG-3000 and citrate pH 5.5]
Temp details: 291 K and 295 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→48.075 Å / Num. obs: 38281 / % possible obs: 99.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 21.76 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Rsym value: 0.06 / Net I/av σ(I): 10.5 / Net I/σ(I): 20.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.960.5191.553020.240.6040.51994.1
1.9-2.026.90.32.552650.1320.3480.3100
2.02-2.157.20.187449830.0810.2170.187100
2.15-2.337.40.1246.146280.0530.1450.124100
2.33-2.557.40.0858.842990.0370.10.085100
2.55-2.857.40.06311.838620.0270.0730.063100
2.85-3.297.30.04515.534260.0190.0520.045100
3.29-4.037.20.03418.729350.0150.040.034100
4.03-5.770.03119.722830.0130.0360.031100
5.7-48.07570.02721.712980.0120.0320.02799.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
SCALA3.3.16data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Unpublished structure of the Se-Met substituted protein

Resolution: 1.8→43 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1674 1914 5 %
Rwork0.1349 36360 -
obs0.1366 38274 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.19 Å2 / Biso mean: 27.1355 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: final / Resolution: 1.8→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 69 470 2965
Biso mean--45.61 38.71 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062707
X-RAY DIFFRACTIONf_angle_d0.8193693
X-RAY DIFFRACTIONf_dihedral_angle_d12.4761005
X-RAY DIFFRACTIONf_chiral_restr0.051371
X-RAY DIFFRACTIONf_plane_restr0.008506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.850.25431090.22572303241288
1.85-1.90.23071200.185626092729100
1.9-1.950.19561220.164426152737100
1.95-2.020.17481060.163726412747100
2.02-2.090.1851550.14825662721100
2.09-2.170.1861460.140525882734100
2.17-2.270.17551710.137225872758100
2.27-2.390.17451280.140226052733100
2.39-2.540.17661470.137126072754100
2.54-2.740.15911470.140426152762100
2.74-3.010.17891330.134126302763100
3.01-3.450.1541540.13626092763100
3.45-4.340.13951260.108726642790100
4.34-430.15811500.119527212871100
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)
12.0623-2.14021.03437.736-1.21436.02720.05550.2824-0.266-0.2501-0.08130.80280.1294-0.62580.00870.1499-0.0379-0.03040.2375-0.02680.180325.6277-5.867253.6917
21.2167-0.12930.19090.8106-0.11310.91740.01450.15740.2009-0.1066-0.0321-0.0407-0.1184-0.0220.0180.13280.01390.0070.12780.01390.147237.160515.063656.9621
32.22460.5010.04012.0911.09231.09570.02860.26580.4497-0.256-0.06880.1381-0.2151-0.16320.04080.17790.0491-0.00390.17790.04550.150720.552919.224652.9596
43.24650.1671.71941.07941.56053.20220.00870.08140.06220.0095-0.03530.18760.0547-0.06860.02280.13760.05450.01720.11080.03280.188326.053115.574255.759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 27 )A11 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 256 )A28 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 298 )A257 - 298
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 326 )A299 - 326

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