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

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Basic information

Entry
Database: PDB / ID: 6nlz
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment degradation product B9D
ComponentsATP-dependent dethiobiotin synthetase BioD
KeywordsTRANSFERASE / 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-KSJ / Chem-KSP / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 degradation product B9D
Authors: Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B.
History
DepositionJan 10, 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)95,89720
Polymers93,1434
Non-polymers2,75516
Water11,115617
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,94910
Polymers46,5712
Non-polymers1,3778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-92 kcal/mol
Surface area17070 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,94910
Polymers46,5712
Non-polymers1,3778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-92 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.610, 105.720, 154.530
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-KSJ / [(1S,2R)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid


Mass: 248.274 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-KSP / [(1R,2S)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid


Mass: 248.274 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
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: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→62.38 Å / Num. obs: 71473 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 22.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.119 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.9413.21.81645440.8110.5171.889100
9.11-62.38120.03375610.010.03499.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.65 Å52.86 Å
Translation7.65 Å52.86 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.6.1phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.306 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.38
RfactorNum. reflection% reflection
Rfree0.2733 3490 4.92 %
Rwork0.2311 --
obs0.2331 70940 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.87 Å2 / Biso mean: 40.5812 Å2 / Biso min: 10.67 Å2
Refinement stepCycle: final / Resolution: 1.9→46.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 184 617 7088
Biso mean--31.68 41.56 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076642
X-RAY DIFFRACTIONf_angle_d0.9679107
X-RAY DIFFRACTIONf_chiral_restr0.0531127
X-RAY DIFFRACTIONf_plane_restr0.0061198
X-RAY DIFFRACTIONf_dihedral_angle_d19.5513914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92610.69331340.68672561269595
1.9261-1.95360.39711310.46242652278398
1.9536-1.98270.36571390.334126272766100
1.9827-2.01370.38151510.310626752826100
2.0137-2.04670.34781450.296726422787100
2.0467-2.0820.31641430.278326892832100
2.082-2.11990.35371370.275626802817100
2.1199-2.16070.33491370.278426822819100
2.1607-2.20480.32271600.279526862846100
2.2048-2.25270.48821450.38472565271097
2.2527-2.30510.37441410.35072611275297
2.3051-2.36270.29031530.271126502803100
2.3627-2.42660.33561370.265426832820100
2.4266-2.4980.32171400.250327122852100
2.498-2.57870.31381250.2527182843100
2.5787-2.67080.31741290.245727112840100
2.6708-2.77770.27621450.244527032848100
2.7777-2.90410.30781550.231327042859100
2.9041-3.05720.26491260.223827272853100
3.0572-3.24870.24761420.216527282870100
3.2487-3.49950.22911320.204627372869100
3.4995-3.85150.24051340.190727682902100
3.8515-4.40840.19211320.160227862918100
4.4084-5.55270.16931290.149928162945100
5.5527-46.31980.17161480.156629373085100

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