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- PDB-4u0p: The Crystal Structure of Lipoyl Synthase in Complex with S-Adenos... -

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Basic information

Entry
Database: PDB / ID: 4u0p
TitleThe Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine
ComponentsLipoyl synthase 2
KeywordsTRANSFERASE / Thiotransferase / TIM barrel / FeS cluster / Radical SAM
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
S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / Lipoyl synthase 2
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.623 Å
Model detailsThermosynechococcus elongatus Lipoyl Synthase 2 in Complex with S-Adenosylhomocysteine
AuthorsHarmer, J.E. / Hiscox, M.J. / Sandy, J. / Dinis, P.C. / 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: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id

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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)33,7165
Polymers32,6051
Non-polymers1,1114
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-55 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.090, 161.130, 59.470
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 / Plasmid: MH003 / 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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, 15% Polyethylene glycol 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: 1.7372 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7372 Å / Relative weight: 1
ReflectionResolution: 1.62→43.89 Å / Num. obs: 43406 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 27.52 Å2 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.023 / Net I/σ(I): 16.9 / Num. measured all: 313330
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
1.62-1.677.10.7572.82250131580.31999.3
7.26-43.895.40.02234.729975570.01999

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
xia2data reduction
SCALAdata scaling
xia2data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.623→43.889 Å / FOM work R set: 0.7933 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 2183 5.03 %Random selection
Rwork0.1781 41197 --
obs0.1795 43380 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.8 Å2 / Biso mean: 37.08 Å2 / Biso min: 23.12 Å2
Refinement stepCycle: final / Resolution: 1.623→43.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 34 172 2367
Biso mean--41.9 42.16 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0242248
X-RAY DIFFRACTIONf_angle_d2.193068
X-RAY DIFFRACTIONf_chiral_restr0.077344
X-RAY DIFFRACTIONf_plane_restr0.009397
X-RAY DIFFRACTIONf_dihedral_angle_d14.62830
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 (%)
1.6234-1.65870.34581200.28522564268499
1.6587-1.69730.27731420.25142497263999
1.6973-1.73980.241380.22652522266099
1.7398-1.78680.24191450.20132526267199
1.7868-1.83940.25651250.19892530265599
1.8394-1.89880.22651350.188925662701100
1.8988-1.96660.22891310.19182549268099
1.9666-2.04540.20191190.176525882707100
2.0454-2.13850.23211670.180125142681100
2.1385-2.25120.2171610.182525392700100
2.2512-2.39220.21581160.178226132729100
2.3922-2.57690.23541120.182926052717100
2.5769-2.83620.2251310.192725992730100
2.8362-3.24650.20761540.194625952749100
3.2465-4.08980.20051690.175726182787100
4.0898-43.90530.16851180.151827722890100

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