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

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Basic information

Entry
Database: PDB / ID: 6nve
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 7
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-L4M / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 7
Authors: Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B.
History
DepositionFeb 5, 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)94,57612
Polymers93,1434
Non-polymers1,4338
Water19,7441096
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2886
Polymers46,5712
Non-polymers7174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-50 kcal/mol
Surface area16850 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2886
Polymers46,5712
Non-polymers7174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-48 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.660, 104.420, 153.510
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WPQ5, dethiobiotin synthase
#2: Chemical
ChemComp-L4M / 4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}benzoic acid


Mass: 262.301 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H18O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1096 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
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→43.17 Å / Num. obs: 59232 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.033 / Rrim(I) all: 0.088 / Net I/σ(I): 15 / Num. measured all: 418592 / Scaling rejects: 1199
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
2-2.057.10.2083086643210.9810.0830.2246.8100
8.94-43.175.50.0441387520.9990.0180.04424.998.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6cve


Resolution: 2→40.53 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 2972 5.04 %
Rwork0.1772 56020 -
obs0.1799 58992 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.67 Å2 / Biso mean: 18.5699 Å2 / Biso min: 3.49 Å2
Refinement stepCycle: final / Resolution: 2→40.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 0 96 1096 7465
Biso mean--11.16 25.85 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066520
X-RAY DIFFRACTIONf_angle_d0.8398935
X-RAY DIFFRACTIONf_chiral_restr0.0511116
X-RAY DIFFRACTIONf_plane_restr0.0061178
X-RAY DIFFRACTIONf_dihedral_angle_d20.7253880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03280.261320.196726232755100
2.0328-2.06780.29121650.184926162781100
2.0678-2.10540.28661490.187126222771100
2.1054-2.14590.27091300.186326812811100
2.1459-2.18970.2711270.208426022729100
2.1897-2.23730.36721520.27762608276098
2.2373-2.28940.2831230.22172580270398
2.2894-2.34660.2591380.186226542792100
2.3466-2.41010.21381430.181326312774100
2.4101-2.4810.26011250.182626692794100
2.481-2.5610.29041640.189126502814100
2.561-2.65260.28181280.185526622790100
2.6526-2.75870.21931370.180326702807100
2.7587-2.88430.22541500.179926522802100
2.8843-3.03630.24471240.183326792803100
3.0363-3.22640.2391500.183326882838100
3.2264-3.47540.23811390.170426952834100
3.4754-3.82490.22131240.163627212845100
3.8249-4.37790.15521500.137727112861100
4.3779-5.51340.15711510.142427542905100
5.5134-40.53870.19691710.15712852302399

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