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

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Basic information

Entry
Database: PDB / ID: 6czc
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with thymidine triphosphate (TTP) - promiscuous binding mode with disordered nucleoside
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsThompson, A.P. / Wegener, K.L. / Bruning, J.B. / Polyak, S.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1068885 Australia
CitationJournal: Acs Catalysis / Year: 2018
Title: Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes
Authors: Thompson, A.P. / Salaemae, W. / Pederick, J.L. / Abell, A.D. / Booker, G.W. / Bruning, J.B. / Polyak, S.W.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)95,92212
Polymers93,8964
Non-polymers2,0268
Water16,664925
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9616
Polymers46,9482
Non-polymers1,0134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-35 kcal/mol
Surface area18020 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9616
Polymers46,9482
Non-polymers1,0134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-43 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.580, 105.370, 154.970
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: 23473.914 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2 - 1.7M ammonium sulfate, 0.1M Tris pH 8 and 10 - 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→46.38 Å / Num. obs: 39064 / % possible obs: 97 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.09 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.049 / Rrim(I) all: 0.13 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.386.10.52937400.9210.2160.57395.4
8.91-46.386.20.0337020.9930.0150.03793

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→36.362 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.21
RfactorNum. reflection% reflection
Rfree0.2726 1914 4.91 %
Rwork0.1838 --
obs0.1881 38968 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.12 Å2 / Biso mean: 26.4862 Å2 / Biso min: 0.89 Å2
Refinement stepCycle: final / Resolution: 2.3→36.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6256 0 120 925 7301
Biso mean--37.04 32.42 -
Num. residues----907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076535
X-RAY DIFFRACTIONf_angle_d1.0318981
X-RAY DIFFRACTIONf_chiral_restr0.0521118
X-RAY DIFFRACTIONf_plane_restr0.0061171
X-RAY DIFFRACTIONf_dihedral_angle_d21.1163905
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.34241360.21262552268895
2.3575-2.42130.29341380.20522559269795
2.4213-2.49250.32651220.20352618274095
2.4925-2.57290.29161390.19762601274096
2.5729-2.66490.32951230.19922598272196
2.6649-2.77150.27921510.19762620277196
2.7715-2.89760.28461390.19332659279897
2.8976-3.05030.27971370.18952673281097
3.0503-3.24130.27141240.19372656278097
3.2413-3.49140.31381430.1972674281797
3.4914-3.84240.34071360.20782645278196
3.8424-4.39760.24661300.172684281496
4.3976-5.53740.21691490.1472740288997
5.5374-36.3670.18441470.15142775292294

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