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- PDB-4u0o: Crystal structure of Thermosynechococcus elongatus Lipoyl Synthas... -

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Basic information

Entry
Database: PDB / ID: 4u0o
TitleCrystal structure of Thermosynechococcus elongatus Lipoyl Synthase 2 complexed with MTA and DTT
ComponentsLipoyl synthase 2
KeywordsTRANSFERASE / radical SAM / TIM barrel / sulfotransferase
Function / homology
Function and homology information


lipoyl synthase / lipoate synthase activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
Lipoyl synthase / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 5'-DEOXY-5'-METHYLTHIOADENOSINE / IRON/SULFUR CLUSTER / Lipoyl synthase 2
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsHarmer, J.E. / Hiscox, M.J. / Dinis, P.C. / Sandy, J. / Roach, P.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J017302/1 United Kingdom
CitationJournal: Biochem.J. / Year: 2014
Title: Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions.
Authors: Harmer, J.E. / Hiscox, M.J. / Dinis, P.C. / Fox, S.J. / Iliopoulos, A. / Hussey, J.E. / Sandy, J. / Van Beek, F.T. / Essex, J.W. / Roach, P.L.
History
DepositionJul 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 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
B: Lipoyl synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7605
Polymers32,6051
Non-polymers1,1554
Water3,261181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-49 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.880, 162.800, 58.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailsbiological unit is the same as asym.

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Components

#1: Protein Lipoyl synthase 2 / / Lip-syn 2 / Lipoate synthase 2 / Lipoic acid synthase 2 / Sulfur insertion protein lipA2


Mass: 32605.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: lipA2, tll0574 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DLC2, lipoyl synthase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM bicine pH 8.5, 15% PEG 20,000, 3% dextran sulfate sodium salt

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→64.99 Å / Num. obs: 44264 / % possible obs: 98.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 27.38 Å2 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.025 / Net I/σ(I): 15 / Num. measured all: 194222
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.6-1.644.70.6012.11531932680.36298.6
7.16-64.994.30.03142.424475660.02398.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å64.62 Å
Translation2.5 Å64.62 Å

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Processing

Software
NameVersionClassification
Cootmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0P

4u0p


Resolution: 1.6→64.988 Å / FOM work R set: 0.7454 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 2229 5.05 %Random selection
Rwork0.2027 41943 --
obs0.2045 44172 97.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.88 Å2 / Biso mean: 36.78 Å2 / Biso min: 19.16 Å2
Refinement stepCycle: final / Resolution: 1.6→64.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 69 181 2305
Biso mean--34.87 41.28 -
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172164
X-RAY DIFFRACTIONf_angle_d1.9582959
X-RAY DIFFRACTIONf_chiral_restr0.085339
X-RAY DIFFRACTIONf_plane_restr0.008377
X-RAY DIFFRACTIONf_dihedral_angle_d14.224782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63480.441270.36742628275598
1.6348-1.67280.36431480.34762586273498
1.6728-1.71470.3481410.31682608274999
1.7147-1.7610.35671350.29462557269297
1.761-1.81290.29861480.27962594274298
1.8129-1.87140.3261570.25232591274898
1.8714-1.93830.28791120.24582474258693
1.9383-2.01590.23731660.21572583274997
2.0159-2.10760.27791340.2212520265495
2.1076-2.21880.26221400.20782659279999
2.2188-2.35780.25971170.20522627274497
2.3578-2.53980.2481370.1952669280699
2.5398-2.79540.22971260.19792659278598
2.7954-3.19990.21471550.20232669282499
3.1999-4.03150.20241550.1862677283298
4.0315-65.04130.23431310.17632842297399

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