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- PDB-5exj: Crystal structure of M. tuberculosis lipoyl synthase at 1.64 A re... -

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Basic information

Entry
Database: PDB / ID: 5exj
TitleCrystal structure of M. tuberculosis lipoyl synthase at 1.64 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 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 / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
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 1.5Sep 27, 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
A: Lipoyl synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7974
Polymers36,9401
Non-polymers8583
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.568, 58.517, 98.772
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.: 328 / 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: 1.9 Å3/Da / Density % sol: 35.26 % / Description: rectangular plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.02 M citric acid, 0.08 M Bis-Tris propane, pH 8.8, 16% (w/v) PEG 3350 in drop; 0.5 M LiCl in reservoir
PH range: 8.8 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.64→100 Å / Num. obs: 35999 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 16.61 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.037 / Rrim(I) all: 0.105 / Χ2: 1.009 / Net I/av σ(I): 19.8 / Net I/σ(I): 5.4 / Num. measured all: 270682
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.64-1.676.20.60917600.7810.260.6640.65599.7
1.67-1.76.90.56918010.8610.2290.6140.68399.8
1.7-1.737.40.51517330.8880.2020.5550.72499.8
1.73-1.777.40.43817640.9130.1710.4710.73199.7
1.77-1.817.30.35817910.9390.1410.3860.80499.7
1.81-1.8570.29917630.9570.120.3240.77399.8
1.85-1.897.90.26617670.9720.1010.2850.815100
1.89-1.9480.22817900.9820.0850.2440.86399.9
1.94-27.90.19517680.9820.0730.2090.90399.8
2-2.077.80.17317850.9810.0660.1850.93699.9
2.07-2.147.60.15318050.9880.0580.1641.009100
2.14-2.236.90.13817910.9910.0550.1491.11999.9
2.23-2.338.10.12718000.9920.0470.1361.123100
2.33-2.458.10.11817940.9910.0440.1261.11499.8
2.45-2.67.90.10918030.9930.0410.1161.11299.9
2.6-2.87.40.09817970.9950.0380.1051.19399.9
2.8-3.097.70.08618420.9950.0320.0921.30799.8
3.09-3.5380.07318270.9970.0270.0781.41899.9
3.53-4.457.30.06218630.9970.0240.0661.42299.6
4.45-1007.40.05619550.9970.0210.061.26498.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å50.34 Å
Translation3 Å50.34 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EXI

5exi


Resolution: 1.64→50.345 Å / FOM work R set: 0.8668 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 1752 4.99 %Random selection
Rwork0.161 33349 --
obs0.1628 35101 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.78 Å2 / Biso mean: 22.78 Å2 / Biso min: 9.44 Å2
Refinement stepCycle: final / Resolution: 1.64→50.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 25 328 2541
Biso mean--19.4 32.32 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012401
X-RAY DIFFRACTIONf_angle_d1.2533303
X-RAY DIFFRACTIONf_chiral_restr0.055361
X-RAY DIFFRACTIONf_plane_restr0.007438
X-RAY DIFFRACTIONf_dihedral_angle_d14.612943
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6401-1.68440.25521300.2322502263299
1.6844-1.7340.25681310.20782517264899
1.734-1.78990.20961320.19012498263099
1.7899-1.85390.21831330.181325452678100
1.8539-1.92810.23731320.164125302662100
1.9281-2.01590.20151350.161325702705100
2.0159-2.12220.17671330.157525302663100
2.1222-2.25510.1871350.147425592694100
2.2551-2.42930.18161350.155725742709100
2.4293-2.67370.1811350.166225742709100
2.6737-3.06060.22791370.169825892726100
3.0606-3.85580.19711380.155426252763100
3.8558-50.36860.17731460.14372736288299

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