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- PDB-5exk: Crystal structure of M. tuberculosis lipoyl synthase with 6-thioo... -

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Basic information

Entry
Database: PDB / ID: 5exk
TitleCrystal structure of M. tuberculosis lipoyl synthase with 6-thiooctanoyl peptide intermediate
Components
  • Lipoyl synthase
  • Octanoylated peptide from M. tuberculosis H protein
KeywordsTRANSFERASE / auxiliary iron-sulfur cluster / AdoMet radical / radical SAM / sulfur insertion
Function / homology
Function and homology information


lipoyl synthase / lipoate synthase activity / glycine cleavage complex / glycine decarboxylation via glycine cleavage system / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Lipoyl synthase, N-terminal / N-terminal domain of lipoyl synthase of Radical_SAM family / Lipoyl synthase / Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / 2-oxo acid dehydrogenase, lipoyl-binding site ...Lipoyl synthase, N-terminal / N-terminal domain of lipoyl synthase of Radical_SAM family / Lipoyl synthase / Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / 2-oxo acid dehydrogenase, lipoyl-binding site / Radical SAM superfamily / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / Radical SAM core domain profile. / Radical SAM / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Aldolase-type TIM barrel
Similarity search - Domain/homology
5'-DEOXYADENOSINE / FE3-S4 CLUSTER / IMIDAZOLE / ISOPROPYL ALCOHOL / METHIONINE / IRON/SULFUR CLUSTER / Lipoyl synthase / Glycine cleavage system H protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoyl synthase
B: Octanoylated peptide from M. tuberculosis H protein
C: Lipoyl synthase
D: Octanoylated peptide from M. tuberculosis H protein
E: Lipoyl synthase
F: Octanoylated peptide from M. tuberculosis H protein
G: Lipoyl synthase
H: Octanoylated peptide from M. tuberculosis H protein
I: Lipoyl synthase
J: Octanoylated peptide from M. tuberculosis H protein
K: Lipoyl synthase
L: Octanoylated peptide from M. tuberculosis H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,25741
Polymers227,70012
Non-polymers6,55629
Water38,5342139
1
A: Lipoyl synthase
B: Octanoylated peptide from M. tuberculosis H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1028
Polymers37,9502
Non-polymers1,1526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-48 kcal/mol
Surface area12820 Å2
MethodPISA
2
C: Lipoyl synthase
D: Octanoylated peptide from M. tuberculosis H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0587
Polymers37,9502
Non-polymers1,1085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-43 kcal/mol
Surface area12630 Å2
MethodPISA
3
E: Lipoyl synthase
F: Octanoylated peptide from M. tuberculosis H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0677
Polymers37,9502
Non-polymers1,1175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-38 kcal/mol
Surface area12650 Å2
MethodPISA
4
G: Lipoyl synthase
H: Octanoylated peptide from M. tuberculosis H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9986
Polymers37,9502
Non-polymers1,0484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-42 kcal/mol
Surface area11950 Å2
MethodPISA
5
I: Lipoyl synthase
J: Octanoylated peptide from M. tuberculosis H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9986
Polymers37,9502
Non-polymers1,0484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-43 kcal/mol
Surface area12540 Å2
MethodPISA
6
K: Lipoyl synthase
L: Octanoylated peptide from M. tuberculosis H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0337
Polymers37,9502
Non-polymers1,0835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-51 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.773, 95.971, 114.328
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

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


Mass: 36939.906 Da / Num. of mol.: 6
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: Protein/peptide
Octanoylated peptide from M. tuberculosis H protein


Mass: 1010.119 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: crosslinked with [3Fe-4S] cluster / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: P9WN55*PLUS

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Non-polymers , 8 types, 2168 molecules

#3: Chemical
ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe3S4
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Fragment: Lipoyl-binding loop / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N5O3
#6: Chemical
ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H11NO2S
#7: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2139 / 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: 1.99 Å3/Da / Density % sol: 38.07 % / Description: thin rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2% Tacsimate pH 7.0, 0.1 M imidazole pH 7.0, 8% (w/v) PEG 3350, 5% (v/v) isopropanol
PH range: 7 / Temp details: room controlled between 291-294 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 143268 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 15.73 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 4.6
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 3 % / Rmerge(I) obs: 0.415 / % possible all: 95.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å47.03 Å
Translation2.5 Å47.03 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→47.03 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 7128 4.98 %Random selection
Rwork0.16 ---
obs0.162 143020 96.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.49 Å2
Refinement stepCycle: LAST / Resolution: 1.86→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14082 0 262 2139 16483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114936
X-RAY DIFFRACTIONf_angle_d1.35420424
X-RAY DIFFRACTIONf_dihedral_angle_d14.8545598
X-RAY DIFFRACTIONf_chiral_restr0.0482281
X-RAY DIFFRACTIONf_plane_restr0.0062750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8614-1.88250.28032080.22553967X-RAY DIFFRACTION85
1.8825-1.90470.31992330.21514465X-RAY DIFFRACTION96
1.9047-1.92790.26562350.19844490X-RAY DIFFRACTION97
1.9279-1.95230.25312300.19224526X-RAY DIFFRACTION97
1.9523-1.9780.24472390.18964481X-RAY DIFFRACTION97
1.978-2.00510.25232400.19344564X-RAY DIFFRACTION97
2.0051-2.03370.2752320.19194497X-RAY DIFFRACTION97
2.0337-2.06410.21892290.18284367X-RAY DIFFRACTION94
2.0641-2.09630.23012420.1744558X-RAY DIFFRACTION97
2.0963-2.13070.20592340.16864571X-RAY DIFFRACTION97
2.1307-2.16740.20732340.16874523X-RAY DIFFRACTION97
2.1674-2.20680.22852350.16194573X-RAY DIFFRACTION97
2.2068-2.24930.222390.1594532X-RAY DIFFRACTION98
2.2493-2.29520.20972350.15774617X-RAY DIFFRACTION98
2.2952-2.34510.22742370.1634524X-RAY DIFFRACTION98
2.3451-2.39970.19552450.16794590X-RAY DIFFRACTION98
2.3997-2.45970.20142350.16434506X-RAY DIFFRACTION97
2.4597-2.52620.21272440.16034438X-RAY DIFFRACTION95
2.5262-2.60050.21942390.16014557X-RAY DIFFRACTION98
2.6005-2.68440.21912430.16594603X-RAY DIFFRACTION98
2.6844-2.78040.24312430.16644612X-RAY DIFFRACTION98
2.7804-2.89170.20992450.16814612X-RAY DIFFRACTION99
2.8917-3.02330.20132390.15994608X-RAY DIFFRACTION98
3.0233-3.18260.20622490.15674590X-RAY DIFFRACTION98
3.1826-3.3820.18582240.14844468X-RAY DIFFRACTION95
3.382-3.6430.16162470.14494665X-RAY DIFFRACTION99
3.643-4.00940.17032470.13974662X-RAY DIFFRACTION99
4.0094-4.58920.13842500.13294636X-RAY DIFFRACTION98
4.5892-5.78020.16362400.14044506X-RAY DIFFRACTION95
5.7802-47.0420.16092360.15034584X-RAY DIFFRACTION95

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