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

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Basic information

Entry
Database: PDB / ID: 6nwn
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with glutamic acid linked compound 10
ComponentsATP-dependent dethiobiotin synthetase BioD
KeywordsTRANSFERASE / enzyme / 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
CITRIC ACID / Chem-L6M / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.005 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 glutamic acid linked compound 10
Authors: Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 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)95,16610
Polymers93,1434
Non-polymers2,0246
Water9,314517
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5835
Polymers46,5712
Non-polymers1,0123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-11 kcal/mol
Surface area17280 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5835
Polymers46,5712
Non-polymers1,0123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-9 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.712, 104.614, 153.628
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-L6M / 5'-{[N-({(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetyl)-L-gamma-glutamyl]amino}-2',5'-dideoxycytidine


Mass: 627.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H37N5O10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.7 M sodium citrate, 0.1 M Tris pH 7 and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.48 Å / Num. obs: 59942 / % possible obs: 99.7 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.019 / Rrim(I) all: 0.072 / Net I/σ(I): 16.9 / Num. measured all: 812798 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0612.30.7825223342310.8890.2290.8162.596.7
8.97-48.4811.80.04191927780.9990.0120.04343.899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CVE

6cve


Resolution: 2.005→46.234 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.71
RfactorNum. reflection% reflection
Rfree0.2255 3026 5.05 %
Rwork0.1842 --
obs0.1863 59869 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.97 Å2 / Biso mean: 39.8015 Å2 / Biso min: 18.59 Å2
Refinement stepCycle: final / Resolution: 2.005→46.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6277 0 142 517 6936
Biso mean--46.54 43.46 -
Num. residues----908
LS refinement shellResolution: 2.0055→2.0368 Å
RfactorNum. reflection% reflection
Rfree0.3433 --
Rwork0.3014 --
obs-2467 96 %

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