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- PDB-3fgn: Crystal structure of dethiobiotin synthetase in Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 3fgn
TitleCrystal structure of dethiobiotin synthetase in Mycobacterium tuberculosis
ComponentsDethiobiotin synthetase
KeywordsLIGASE / dethiobiotin synthetase / biotin biosynthesis / bioD / ATP-binding / Magnesium / Nucleotide-binding
Function / homology
Function and homology information


dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Dethiobiotin synthase BioD / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent dethiobiotin synthetase BioD / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.85 Å
AuthorsDey, S. / Sacchettini, J.C.
CitationJournal: Biochemistry / Year: 2010
Title: Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .
Authors: Dey, S. / Lane, J.M. / Lee, R.E. / Rubin, E.J. / Sacchettini, J.C.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dethiobiotin synthetase
B: Dethiobiotin synthetase
C: Dethiobiotin synthetase
D: Dethiobiotin synthetase


Theoretical massNumber of molelcules
Total (without water)101,2644
Polymers101,2644
Non-polymers00
Water5,765320
1
A: Dethiobiotin synthetase
B: Dethiobiotin synthetase


Theoretical massNumber of molelcules
Total (without water)50,6322
Polymers50,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-14 kcal/mol
Surface area17630 Å2
MethodPISA
2
C: Dethiobiotin synthetase
D: Dethiobiotin synthetase


Theoretical massNumber of molelcules
Total (without water)50,6322
Polymers50,6322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-14 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.383, 104.684, 151.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Dethiobiotin synthetase / Dethiobiotin synthase / DTB synthetase / DTBS


Mass: 25315.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: bioD, MT1621, MTCY336.33c, Rv1570 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O06620, UniProt: P9WPQ5*PLUS, dethiobiotin synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1M sodium citrate, 0.1M imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.85→31.7 Å / Num. obs: 73740 / % possible obs: 99 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / % possible all: 93.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SHARPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→31.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.527 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: SAD (SAMARIUM) USED FOR STRUCTURE DETERMINATION
RfactorNum. reflection% reflectionSelection details
Rfree0.25332 3705 5 %RANDOM
Rwork0.21436 ---
obs0.21632 70111 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.247 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2--0.8 Å20 Å2
3----2.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 0 320 6638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226407
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9788763
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97923.317205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12715933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8811553
X-RAY DIFFRACTIONr_chiral_restr0.0870.21105
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024772
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.32914
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.54389
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5592
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.373
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.29554570
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.19677077
X-RAY DIFFRACTIONr_scbond_it4.58892008
X-RAY DIFFRACTIONr_scangle_it6.161111686
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.523 190 -
Rwork0.446 3858 -
obs--73.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64240.47760.19130.35810.1950.987-0.0079-0.0523-0.06660.0153-0.0146-0.0496-0.0256-0.03940.0225-0.09130.02720.0026-0.0665-0.0198-0.0986-8.948427.5628-16.429
20.74880.5448-0.28090.43860.0251.351-0.0237-0.0351-0.05360.03270.01280.05070.09990.10350.0108-0.07260.01230.0068-0.0962-0.0177-0.11184.612217.1703-42.6046
32.15410.17120.00290.86190.39441.2490.00470.05280.0594-0.0252-0.06760.0252-0.1093-0.08930.0629-0.06770.0481-0.0144-0.1402-0.0241-0.1498-28.6497-4.8633-22.6574
40.1278-0.0949-0.27820.5367-0.2182.26230.10330.01280.05090.0058-0.1035-0.07620.18280.24410.00020.03910.0368-0.01370.03960.0311-0.0382-16.6625-7.0786.6339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 226
2X-RAY DIFFRACTION2B1 - 225
3X-RAY DIFFRACTION3C1 - 226
4X-RAY DIFFRACTION4D2 - 225

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