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- PDB-6nl4: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -

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Basic information

Entry
Database: PDB / ID: 6nl4
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with gemcitabine
ComponentsATP-dependent dethiobiotin synthetase BioD
KeywordsTRANSFERASE/ANTIBIOTIC / enzyme / synthetase / nucleotide triphosphate binding / TRANSFERASE / TRANSFERASE-ANTIBIOTIC complex
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
GEMCITABINE / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.991 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 gemcitabine
Authors: Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)94,31711
Polymers93,1434
Non-polymers1,1747
Water14,664814
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2906
Polymers46,5712
Non-polymers7194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-51 kcal/mol
Surface area17040 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0275
Polymers46,5712
Non-polymers4553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-45 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.514, 106.076, 151.951
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GEO / GEMCITABINE / 2',2'-DIFLUORODEOXYCYTIDINE


Mass: 263.198 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11F2N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
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: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.99→46.8 Å / Num. obs: 62085 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 32.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 13.8 / Num. measured all: 448314
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
1.99-2.0470.8073036843140.8850.3220.87295.4
8.91-46.85.80.021464879510.0090.0234498

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.29data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.991→38.349 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 3090 4.99 %
Rwork0.1969 58795 -
obs0.1996 61885 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.63 Å2 / Biso mean: 36.0319 Å2 / Biso min: 8.21 Å2
Refinement stepCycle: final / Resolution: 1.991→38.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6271 0 74 814 7159
Biso mean--49.63 40.76 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076544
X-RAY DIFFRACTIONf_angle_d0.8678987
X-RAY DIFFRACTIONf_chiral_restr0.0541122
X-RAY DIFFRACTIONf_plane_restr0.0061185
X-RAY DIFFRACTIONf_dihedral_angle_d19.4223892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9913-2.02240.38921110.29722444255592
2.0224-2.05560.30121560.266226532809100
2.0556-2.0910.3111500.245126112761100
2.091-2.1290.32121360.23726892825100
2.129-2.170.33951570.252326032760100
2.17-2.21420.33491660.305726512817100
2.2142-2.26240.46121230.36482587271098
2.2624-2.3150.43021410.3462634277599
2.315-2.37290.30721370.237726202757100
2.3729-2.4370.26441470.199326912838100
2.437-2.50870.23211280.189626782806100
2.5087-2.58970.26041460.19726552801100
2.5897-2.68220.24791300.194726762806100
2.6822-2.78960.24521360.198327132849100
2.7896-2.91650.25041320.204126812813100
2.9165-3.07020.3111350.20127002835100
3.0702-3.26250.26981370.195726952832100
3.2625-3.51420.22621280.178627172845100
3.5142-3.86760.24571510.18326932844100
3.8676-4.42650.18951550.147127262881100
4.4265-5.57420.17261470.148227852932100
5.5742-38.35610.21881410.1752893303499

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