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

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Basic information

Entry
Database: PDB / ID: 6nvf
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 8
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-L5A / Chem-L5J / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.989 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 8
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)95,18514
Polymers93,1434
Non-polymers2,04210
Water15,403855
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5927
Polymers46,5712
Non-polymers1,0215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-50 kcal/mol
Surface area16980 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5927
Polymers46,5712
Non-polymers1,0215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-49 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.401, 104.342, 154.297
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPQ5, dethiobiotin synthase
#2: Chemical
ChemComp-L5A / (4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid


Mass: 276.328 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20O4 / 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: Chemical ChemComp-L5J / (4-{[(1R,2R)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid


Mass: 276.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
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: 1.99→46.13 Å / Num. obs: 61199 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 28.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Net I/σ(I): 13.1 / Num. measured all: 443844
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
1.99-2.0470.7712903541320.8710.3080.8311.896.4
9.11-46.135.90.02443327400.9990.010.02642.199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CVE

6cve


Resolution: 1.989→46.132 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 3108 5.1 %
Rwork0.1849 57816 -
obs0.1874 60924 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.4 Å2 / Biso mean: 30.7984 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 1.989→46.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6292 0 140 855 7287
Biso mean--23.43 36.03 -
Num. residues----909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066555
X-RAY DIFFRACTIONf_angle_d0.8618972
X-RAY DIFFRACTIONf_chiral_restr0.051116
X-RAY DIFFRACTIONf_plane_restr0.0051178
X-RAY DIFFRACTIONf_dihedral_angle_d19.8393878
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 (%)
1.9888-2.01990.33781300.25922500263095
2.0199-2.0530.30141380.226225782716100
2.053-2.08840.30571380.208126372775100
2.0884-2.12640.23261240.198225892713100
2.1264-2.16720.26481330.211226142747100
2.1672-2.21150.28981230.26392611273499
2.2115-2.25960.49661190.39552476259594
2.2596-2.31210.29691410.235925922733100
2.3121-2.370.27211520.190326402792100
2.37-2.4340.22951520.189425642716100
2.434-2.50560.25181360.18426472783100
2.5056-2.58650.24991320.198626402772100
2.5865-2.67890.26761560.205526042760100
2.6789-2.78620.3021310.201326322763100
2.7862-2.9130.25921330.19626692802100
2.913-3.06650.24481510.190626142765100
3.0665-3.25860.25661340.18926702804100
3.2586-3.51010.20141420.174426502792100
3.5101-3.86320.19861440.165826762820100
3.8632-4.42180.18661580.134126762834100
4.4218-5.56950.1661790.142726862865100
5.5695-46.14480.18151620.156928513013100

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