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- PDB-6nn0: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -

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Basic information

Entry
Database: PDB / ID: 6nn0
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and 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
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / Chem-KSJ / Chem-KSP / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.343 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 2'-deoxycytidine and B9D
Authors: Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B.
History
DepositionJan 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 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

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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)96,28821
Polymers93,1434
Non-polymers3,14517
Water3,315184
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,09610
Polymers46,5712
Non-polymers1,5258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-69 kcal/mol
Surface area17150 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,19211
Polymers46,5712
Non-polymers1,6219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-95 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.490, 106.560, 154.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 201 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: 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
#5: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 48.85 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 5, 2017
RadiationMonochromator: Rigaku VariMax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.34→87.68 Å / Num. obs: 37848 / % possible obs: 97.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 49.81 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.052 / Rrim(I) all: 0.18 / Net I/σ(I): 9.2 / Num. measured all: 440918 / Scaling rejects: 3646
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
2.34-2.4311.92.6064271835880.5370.7682.7220.796.8
9.07-87.6811.50.04388807730.9990.0130.04532.4100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.31data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.343→53.28 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.02
RfactorNum. reflection% reflection
Rfree0.2957 1858 4.94 %
Rwork0.2215 --
obs0.2251 37584 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.03 Å2 / Biso mean: 57.6978 Å2 / Biso min: 20.11 Å2
Refinement stepCycle: final / Resolution: 2.343→53.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 213 184 6659
Biso mean--54.59 48.75 -
Num. residues----907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086592
X-RAY DIFFRACTIONf_angle_d1.0679034
X-RAY DIFFRACTIONf_chiral_restr0.0531126
X-RAY DIFFRACTIONf_plane_restr0.0061179
X-RAY DIFFRACTIONf_dihedral_angle_d19.8993858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3431-2.40640.33381270.31262663279096
2.4064-2.47720.4621450.34482634277994
2.4772-2.55720.42121370.34782643278096
2.5572-2.64860.34961300.31662656278695
2.6486-2.75460.35281360.30322661279795
2.7546-2.880.40291310.30022702283396
2.88-3.03180.36961670.28142710287798
3.0318-3.22170.33221330.27332806293999
3.2217-3.47040.37481440.26022768291299
3.4704-3.81960.31981480.23792759290797
3.8196-4.37210.27081360.17582821295799
4.3721-5.50740.23691630.160228883051100
5.5074-53.29380.19771610.156130153176100

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