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

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Basic information

Entry
Database: PDB / ID: 6nnz
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 4
ComponentsATP-dependent dethiobiotin synthetase BioD
KeywordsTRANSFERASE / enzyme / 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
Chem-KUD / Chem-KUG / 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. / 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 4
Authors: Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)95,76920
Polymers93,1434
Non-polymers2,62716
Water4,792266
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A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,88510
Polymers46,5712
Non-polymers1,3138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-93 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)47,88510
Polymers46,5712
Non-polymers1,3138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-93 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.610, 108.350, 153.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 18 or resid 20...
21(chain B and (resid 0 through 18 or resid 20...
31(chain C and (resid 0 through 18 or resid 20...
41(chain D and (resid 0 through 18 or resid 20...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVAL(chain A and (resid 0 through 18 or resid 20...AA0 - 187 - 25
12ALAALALEULEU(chain A and (resid 0 through 18 or resid 20...AA20 - 15327 - 160
13ALAALAGLNGLN(chain A and (resid 0 through 18 or resid 20...AA155 - 159162 - 166
14GLYGLYGLYGLY(chain A and (resid 0 through 18 or resid 20...AA0 - 2267 - 233
15GLYGLYGLYGLY(chain A and (resid 0 through 18 or resid 20...AA0 - 2267 - 233
16GLYGLYGLYGLY(chain A and (resid 0 through 18 or resid 20...AA0 - 2267 - 233
17GLYGLYGLYGLY(chain A and (resid 0 through 18 or resid 20...AA0 - 2267 - 233
18GLYGLYGLYGLY(chain A and (resid 0 through 18 or resid 20...AA0 - 2267 - 233
19GLYGLYGLYGLY(chain A and (resid 0 through 18 or resid 20...AA0 - 2267 - 233
110GLYGLYGLYGLY(chain A and (resid 0 through 18 or resid 20...AA0 - 2267 - 233
21GLYGLYVALVAL(chain B and (resid 0 through 18 or resid 20...BB0 - 187 - 25
22ALAALAALAALA(chain B and (resid 0 through 18 or resid 20...BB20 - 7827 - 85
23GLYGLYVALVAL(chain B and (resid 0 through 18 or resid 20...BB0 - 2257 - 232
24GLYGLYVALVAL(chain B and (resid 0 through 18 or resid 20...BB0 - 2257 - 232
25GLYGLYVALVAL(chain B and (resid 0 through 18 or resid 20...BB0 - 2257 - 232
26GLYGLYVALVAL(chain B and (resid 0 through 18 or resid 20...BB0 - 2257 - 232
27GLYGLYVALVAL(chain B and (resid 0 through 18 or resid 20...BB0 - 2257 - 232
28GLYGLYVALVAL(chain B and (resid 0 through 18 or resid 20...BB0 - 2257 - 232
31GLYGLYVALVAL(chain C and (resid 0 through 18 or resid 20...CC0 - 187 - 25
32ALAALAALAALA(chain C and (resid 0 through 18 or resid 20...CC20 - 7827 - 85
33GLUGLUGLUGLU(chain C and (resid 0 through 18 or resid 20...CC7986
34GLYGLYGLYGLY(chain C and (resid 0 through 18 or resid 20...CC0 - 2267 - 233
35GLYGLYGLYGLY(chain C and (resid 0 through 18 or resid 20...CC0 - 2267 - 233
36GLYGLYGLYGLY(chain C and (resid 0 through 18 or resid 20...CC0 - 2267 - 233
37GLYGLYGLYGLY(chain C and (resid 0 through 18 or resid 20...CC0 - 2267 - 233
41GLYGLYVALVAL(chain D and (resid 0 through 18 or resid 20...DD0 - 187 - 25
42ALAALAALAALA(chain D and (resid 0 through 18 or resid 20...DD20 - 7827 - 85
43GLUGLUGLUGLU(chain D and (resid 0 through 18 or resid 20...DD7986
44HISHISVALVAL(chain D and (resid 0 through 18 or resid 20...DD-1 - 2256 - 232
45HISHISVALVAL(chain D and (resid 0 through 18 or resid 20...DD-1 - 2256 - 232
46HISHISVALVAL(chain D and (resid 0 through 18 or resid 20...DD-1 - 2256 - 232
47HISHISVALVAL(chain D and (resid 0 through 18 or resid 20...DD-1 - 2256 - 232

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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-KUD / [(1S,2R)-2-(benzenecarbonyl)cyclopentyl]acetic acid


Mass: 232.275 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-KUG / [(1R,2S)-2-(benzenecarbonyl)cyclopentyl]acetic acid


Mass: 232.275 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
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: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→62.7 Å / Num. obs: 39063 / % possible obs: 92.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 37.64 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.058 / Rrim(I) all: 0.204 / Net I/σ(I): 8.6 / Num. measured all: 460196 / Scaling rejects: 2160
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
2.3-2.3811.73.3074547738830.8540.9573.4480.895.8
8.91-62.710.50.06887798370.9970.0220.07222.999.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.91 Å41.6 Å
Translation6.91 Å41.6 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
Aimless0.5.31data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CVE

6cve


Resolution: 2.3→41.603 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2929 1892 4.96 %
Rwork0.2564 36229 -
obs0.2582 38121 90.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.8 Å2 / Biso mean: 47.8084 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 2.3→41.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 176 266 6714
Biso mean--39.49 40.4 -
Num. residues----907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016575
X-RAY DIFFRACTIONf_angle_d1.4849003
X-RAY DIFFRACTIONf_chiral_restr0.0841119
X-RAY DIFFRACTIONf_plane_restr0.0111183
X-RAY DIFFRACTIONf_dihedral_angle_d19.4713875
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3796X-RAY DIFFRACTION17.19TORSIONAL
12B3796X-RAY DIFFRACTION17.19TORSIONAL
13C3796X-RAY DIFFRACTION17.19TORSIONAL
14D3796X-RAY DIFFRACTION17.19TORSIONAL
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 (%)
2.3-2.35750.36971140.35812335244983
2.3575-2.42130.36181390.30272629276893
2.4213-2.49250.38041350.31562648278394
2.4925-2.57290.35431370.30492670280795
2.5729-2.66490.42361520.29282634278694
2.6649-2.77150.35741240.29362105222974
2.7715-2.89770.29751440.28252633277794
2.8977-3.05040.29121320.2732704283695
3.0504-3.24140.35791440.29192713285795
3.2414-3.49160.36841230.29942375249883
3.4916-3.84270.3381090.33522312242181
3.8427-4.39830.31181230.27032507263087
4.3983-5.53930.20721580.18182920307899
5.5393-41.610.19171580.168930443202100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5583-0.9953-0.00661.74670.1412.4891-0.10230.56930.4044-0.31130.0459-0.1431-0.37550.17520.06010.3321-0.05030.00790.29750.0440.245160.7093144.311713.4517
26.2811-0.6569-0.49173.64540.01252.6423-0.18291.5144-0.046-0.6365-0.13510.06310.0322-0.52180.10030.32010.0294-0.01540.5206-0.0480.240356.8375135.89538.172
32.3569-0.4488-0.62732.7115-0.25113.9304-0.0016-0.0365-0.00050.20270.0094-0.29880.08560.72310.04060.23030.03110.0160.3424-0.05310.24470.0393133.526822.055
43.179-1.14410.65521.6222-0.40512.18630.1557-0.0963-0.12990.0489-0.04910.02770.05420.0442-0.09310.3886-0.01010.04270.30260.04380.201854.8998123.775449.1319
51.93990.0122-0.81971.463-0.6395.0556-0.0603-0.03670.0170.21650.23350.2095-0.0949-0.4327-0.17820.34570.06290.04370.33410.01580.232647.1062130.110937.4177
63.91760.34910.21743.2239-0.4412.1408-0.0214-0.27590.05561.1127-0.1391-0.15620.08920.11060.08080.9688-0.1736-0.00980.46080.0660.349279.138100.577727.6443
72.97250.1576-0.62513.2094-0.1172.83410.1231-0.50280.41071.1443-0.08520.1642-0.1914-0.0501-0.08230.6657-0.12680.01010.3978-0.01010.311379.3728110.055423.4588
83.03651.32270.43766.5560.17134.1945-0.12270.00850.06430.1564-0.120.1314-0.1564-0.0833-0.04610.2764-0.01940.0360.31410.03970.266783.0669108.39857.7184
92.28530.2135-0.16182.9013-0.61682.31990.2898-0.1972-0.23891.0726-0.4164-1.07730.4970.54990.07280.7254-0.0057-0.26620.41560.09210.512794.685398.99317.2113
103.449-0.2539-0.47571.14721.82262.9312-0.08880.48040.03280.0819-0.12890.26960.3491-0.11190.18030.4987-0.0714-0.03210.32720.0220.319273.559396.1742-12.6795
113.9934-1.45320.09992.65520.69383.64150.37780.06520.6124-0.3578-0.2828-0.35280.2391-0.0212-0.21320.3830.0629-0.01310.3437-0.0030.262581.717103.6235-15.8905
122.0415-0.74850.29373.1210.52555.0466-0.0525-0.1390.0748-0.12710.0227-0.11090.22630.0114-0.09850.3466-0.01770.01830.2226-0.00460.289776.9338106.9051-0.9858
131.8042-0.8069-0.41861.83910.24564.69440.049-0.2648-0.3560.5275-0.1890.47771.0164-0.55890.03960.4966-0.16760.06040.458-0.00980.431362.772198.53992.7893
142.2421-0.31910.04142.3711.00813.73290.7094-0.4328-0.47260.0547-0.18820.8570.8046-1.12540.09170.5374-0.152-0.12370.71020.01540.57357.653498.976-10.3629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 87 )A0 - 87
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 123 )A88 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 226 )A124 - 226
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 108 )B0 - 108
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 225 )B109 - 225
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 87 )C0 - 87
7X-RAY DIFFRACTION7chain 'C' and (resid 88 through 144 )C88 - 144
8X-RAY DIFFRACTION8chain 'C' and (resid 145 through 159 )C145 - 159
9X-RAY DIFFRACTION9chain 'C' and (resid 160 through 226 )C160 - 226
10X-RAY DIFFRACTION10chain 'D' and (resid -1 through 73 )D-1 - 73
11X-RAY DIFFRACTION11chain 'D' and (resid 74 through 108 )D74 - 108
12X-RAY DIFFRACTION12chain 'D' and (resid 109 through 159 )D109 - 159
13X-RAY DIFFRACTION13chain 'D' and (resid 160 through 204 )D160 - 204
14X-RAY DIFFRACTION14chain 'D' and (resid 205 through 225 )D205 - 225

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