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- PDB-6nu6: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -

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Basic information

Entry
Database: PDB / ID: 6nu6
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 5
ComponentsATP-dependent dethiobiotin synthetase BioD
KeywordsLIGASE / TRANSFERASE / enzyme / synthetase / nucleotide triphosphate binding
Function / homology
Function and homology information


dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol
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
Chem-L1V / Chem-L1Y / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.437 Å
AuthorsThompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1068885 Australia
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 5
Authors: Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B.
History
DepositionJan 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,73716
Polymers93,1434
Non-polymers2,59512
Water3,171176
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8698
Polymers46,5712
Non-polymers1,2976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-50 kcal/mol
Surface area16780 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8698
Polymers46,5712
Non-polymers1,2976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-49 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.797, 105.593, 152.523
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
ATP-dependent dethiobiotin synthetase BioD / DTB synthetase / DTBS / Dethiobiotin synthase


Mass: 23285.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: bioD, Rv1570, MTCY336.33c / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPQ5, dethiobiotin synthase
#2: Chemical
ChemComp-L1V / 4-[(1R,2S)-2-(carboxymethyl)cyclopentane-1-carbonyl]benzoic acid


Mass: 276.285 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H16O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-L1Y / 4-[(1S,2R)-2-(carboxymethyl)cyclopentane-1-carbonyl]benzoic acid


Mass: 276.285 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H16O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 1.2 - 1.7 M ammonium sulfate, 0.1 M Tris pH 8, 10-15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.437→46.34 Å / Num. obs: 33468 / % possible obs: 98.6 % / Redundancy: 14.5 % / Biso Wilson estimate: 52.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.021 / Rrim(I) all: 0.082 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.44-2.53140.90830540.9430.2450.94187.3
9.12-46.3412.20.02174710.0060.02299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CVE

6cve


Resolution: 2.437→46.339 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 29.75
RfactorNum. reflection% reflection
Rfree0.2592 1736 5.2 %
Rwork0.1989 --
obs0.2022 33365 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.56 Å2 / Biso mean: 56.8397 Å2 / Biso min: 27.24 Å2
Refinement stepCycle: final / Resolution: 2.437→46.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 180 176 6638
Biso mean--51.56 49.8 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076565
X-RAY DIFFRACTIONf_angle_d0.9948988
X-RAY DIFFRACTIONf_chiral_restr0.051116
X-RAY DIFFRACTIONf_plane_restr0.0061184
X-RAY DIFFRACTIONf_dihedral_angle_d19.9733868
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4369-2.50860.40311130.2872237235084
2.5086-2.58960.29641290.25732627275699
2.5896-2.68210.34231500.246326082758100
2.6821-2.78950.29391400.230626322772100
2.7895-2.91640.30031350.240726492784100
2.9164-3.07010.36421470.243926552802100
3.0701-3.26240.33181370.243326462783100
3.2624-3.51430.32961430.226226632806100
3.5143-3.86780.26121400.21162680282099
3.8678-4.42710.24241620.167626682830100
4.4271-5.57610.21461790.166227042883100
5.5761-46.34710.1911610.159728603021100

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