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- PDB-5exi: Crystal structure of M. tuberculosis lipoyl synthase at 2.28 A re... -

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Basic information

Entry
Database: PDB / ID: 5exi
TitleCrystal structure of M. tuberculosis lipoyl synthase at 2.28 A resolution
ComponentsLipoyl synthase
KeywordsTRANSFERASE / auxiliary iron-sulfur cluster / AdoMet radical / radical SAM / sulfur insertion
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, N-terminal / N-terminal domain of lipoyl synthase of Radical_SAM family / 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
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / IRON/SULFUR CLUSTER / Lipoyl synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.28 Å
AuthorsMcLaughlin, M.I. / Lanz, N.D. / Goldman, P.J. / Lee, K.-H. / Booker, S.J. / Drennan, C.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM063847 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM103268 United States
National Science Foundation (NSF, United States)MCB-0543833 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103403 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Crystallographic snapshots of sulfur insertion by lipoyl synthase.
Authors: McLaughlin, M.I. / Lanz, N.D. / Goldman, P.J. / Lee, K.H. / Booker, S.J. / Drennan, C.L.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Lipoyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7974
Polymers36,9401
Non-polymers8583
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.663, 57.815, 116.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36939.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lipA, Rv2218, MTCY190.29 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WK91, lipoyl synthase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.22 Å3/Da / Density % sol: 44.63 % / Description: square thin plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 12% (w/v) PEG 10000, 7.5% (v/v) MPD in drop; 0.5 M LiCl in reservoir
PH range: 7.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7389, 1.7418, 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.73891
21.74181
30.97951
ReflectionRedundancy: 8.2 % / Number: 119171 / Rmerge(I) obs: 0.152 / Χ2: 1.17 / D res high: 2.28 Å / D res low: 200 Å / Num. obs: 14576 / % possible obs: 93.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.9120010.0891.1389.3
3.94.9110.1081.1799.5
3.413.910.1371.2459.3
3.093.4110.1821.269.5
2.873.0910.2531.269.6
2.72.8710.3261.1949.3
2.572.710.3991.1118.6
2.462.5710.4431.0696.4
2.362.4610.461.0064.6
2.282.3610.4580.983.6
ReflectionResolution: 2.28→200 Å / Num. obs: 14576 / % possible obs: 93.1 % / Redundancy: 8.2 % / Biso Wilson estimate: 29.23 Å2 / Rmerge(I) obs: 0.152 / Χ2: 1.175 / Net I/av σ(I): 12 / Net I/σ(I): 4.9 / Num. measured all: 119171
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.28-2.363.60.45810160.9866.5
2.36-2.464.60.4613371.00687.4
2.46-2.576.40.44314651.06995.3
2.57-2.78.60.39915121.11197.9
2.7-2.879.30.32615071.19498.1
2.87-3.099.60.25315181.2698.3
3.09-3.419.50.18215331.2698.2
3.41-3.99.30.13715461.24598.1
3.9-4.919.50.10815451.17996.7
4.91-2009.30.08915971.13893.9

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.28 Å / D res low: 51.81 Å / FOM acentric: 0.166 / FOM centric: 0.174 / Reflection acentric: 12707 / Reflection centric: 1977
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.2851.810058861181
ISO_22.2851.810.2390.2845610986
ISO_32.2851.811.0991.08658501046
ANO_12.2851.811.174057940
ANO_22.2851.811.035053720
ANO_32.2851.810.3060120690
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_110.02-51.810010592
ISO_17.15-10.0200222100
ISO_15.86-7.1500326106
ISO_15.08-5.860037490
ISO_14.55-5.0800446104
ISO_14.15-4.5500504101
ISO_13.85-4.150054698
ISO_13.6-3.8500588105
ISO_13.4-3.60062998
ISO_13.22-3.40066098
ISO_13.07-3.220070896
ISO_12.94-3.070072990
ISO_12.83-2.9400493
ISO_12.73-2.830000
ISO_12.63-2.730000
ISO_12.55-2.630000
ISO_12.47-2.550000
ISO_12.4-2.470000
ISO_12.34-2.40000
ISO_12.28-2.340000
ANO_110.02-51.814.75401020
ANO_17.15-10.023.78102180
ANO_15.86-7.152.92103180
ANO_15.08-5.862.05103660
ANO_14.55-5.081.21604390
ANO_14.15-4.550.83605010
ANO_13.85-4.150.605370
ANO_13.6-3.850.42705830
ANO_13.4-3.60.30406210
ANO_13.22-3.40.22406480
ANO_13.07-3.220.17707000
ANO_12.94-3.070.11307170
ANO_12.83-2.940.10440
ANO_12.73-2.830000
ANO_12.63-2.730000
ANO_12.55-2.630000
ANO_12.47-2.550000
ANO_12.4-2.470000
ANO_12.34-2.40000
ANO_12.28-2.340000
ISO_210.02-51.811.0870.8229473
ISO_27.15-10.020.8090.49320079
ISO_25.86-7.150.6030.4929484
ISO_25.08-5.860.4420.29135480
ISO_24.55-5.080.2570.19942689
ISO_24.15-4.550.1770.12847784
ISO_23.85-4.150.1260.10751778
ISO_23.6-3.850.0860.0756789
ISO_23.4-3.60.060.05360681
ISO_23.22-3.40.0450.03364585
ISO_23.07-3.220.0350.02569889
ISO_22.94-3.070.0220.01971375
ISO_22.83-2.940.0150190
ISO_22.73-2.830000
ISO_22.63-2.730000
ISO_22.55-2.630000
ISO_22.47-2.550000
ISO_22.4-2.470000
ISO_22.34-2.40000
ISO_22.28-2.340000
ANO_210.02-51.815.6840880
ANO_27.15-10.023.92101920
ANO_25.86-7.152.91602840
ANO_25.08-5.862.00603340
ANO_24.55-5.081.07704020
ANO_24.15-4.550.78604560
ANO_23.85-4.150.49304960
ANO_23.6-3.850.36605480
ANO_23.4-3.60.26205840
ANO_23.22-3.40.19206120
ANO_23.07-3.220.15306740
ANO_22.94-3.070.10406830
ANO_22.83-2.940.0690190
ANO_22.73-2.830000
ANO_22.63-2.730000
ANO_22.55-2.630000
ANO_22.47-2.550000
ANO_22.4-2.470000
ANO_22.34-2.40000
ANO_22.28-2.340000
ISO_310.02-51.814.4842.67710069
ISO_37.15-10.023.252.02821575
ISO_35.86-7.152.571.82131784
ISO_35.08-5.861.9071.29237178
ISO_34.55-5.081.170.7844295
ISO_34.15-4.550.8110.61850092
ISO_33.85-4.150.6150.43254387
ISO_33.6-3.850.4290.30958797
ISO_33.4-3.60.3260.25862992
ISO_33.22-3.40.2340.15966093
ISO_33.07-3.220.1760.11870894
ISO_32.94-3.070.1140.09772987
ISO_32.83-2.940.1210.099493
ISO_32.73-2.830000
ISO_32.63-2.730000
ISO_32.55-2.630000
ISO_32.47-2.550000
ISO_32.4-2.470000
ISO_32.34-2.40000
ISO_32.28-2.340000
ANO_310.02-51.812.78801090
ANO_37.15-10.021.88602300
ANO_35.86-7.151.53103180
ANO_35.08-5.860.94203880
ANO_34.55-5.080.56804510
ANO_34.15-4.550.41305020
ANO_33.85-4.150.30505560
ANO_33.6-3.850.20805910
ANO_33.4-3.60.14806440
ANO_33.22-3.40.10706800
ANO_33.07-3.220.07607230
ANO_32.94-3.070.04607590
ANO_32.83-2.940.03507820
ANO_32.73-2.830.02408020
ANO_32.63-2.730.01708460
ANO_32.55-2.630.01208440
ANO_32.47-2.550.00808590
ANO_32.4-2.470.00608270
ANO_32.34-2.40.00506610
ANO_32.28-2.340.00304970
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-23.094-15.727-10.87FE141.033.26
2-13.737-15.693-25.867FE129.063.12
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
10.02-51.810.8670.63311898
7.15-10.020.8260.55242111
5.86-7.150.7720.515332109
5.08-5.860.6720.372397105
4.55-5.080.5280.334459107
4.15-4.550.4430.209512109
3.85-4.150.3310.163567106
3.6-3.850.2580.12598109
3.4-3.60.2030.091652114
3.22-3.40.1570.069686105
3.07-3.220.1210.063731104
2.94-3.070.0950.064771110
2.83-2.940.0320.019791110
2.73-2.830.0190.01381899
2.63-2.730.0120.008869110
2.55-2.630.0080.005878101
2.47-2.550.0050.00389895
2.4-2.470.0030.00291691
2.34-2.40.0020.00280347
2.28-2.340.0010.00166937

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
SHARPphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 2.28→58.284 Å / FOM work R set: 0.8228 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.213 714 4.89 %Random selection
Rwork0.1634 25275 --
obs0.166 13102 91.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.71 Å2 / Biso mean: 34.63 Å2 / Biso min: 19.05 Å2
Refinement stepCycle: final / Resolution: 2.28→58.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 24 216 2399
Biso mean--30.74 40.88 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072240
X-RAY DIFFRACTIONf_angle_d1.0043056
X-RAY DIFFRACTIONf_chiral_restr0.068336
X-RAY DIFFRACTIONf_plane_restr0.004400
X-RAY DIFFRACTIONf_dihedral_angle_d14.959846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2801-2.37140.317850.24111853193861
2.3714-2.47930.31981300.2322664279487
2.4793-2.61010.28351580.21182904306294
2.6101-2.77360.26131460.21012963310997
2.7736-2.98770.26091600.19213001316198
2.9877-3.28840.26111590.18543023318298
3.2884-3.76410.17531630.14193003316698
3.7641-4.74210.18521520.12582981313398
4.7421-58.3030.14371470.12922883303094

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