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- PDB-6e06: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -

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Basic information

Entry
Database: PDB / ID: 6000000
TitleCrystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine triphosphate solved by precipitant-ligand exchange (crystals grown in citrate precipitant)
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
CYTIDINE-5'-TRIPHOSPHATE / Dethiobiotin synthetase BioD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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: Acta Crystallogr D Struct Biol / Year: 2018
Title: Precipitant-ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase.
Authors: Thompson, A.P. / Wegener, K.L. / Booker, G.W. / Polyak, S.W. / Bruning, J.B.
History
DepositionJul 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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)95,92612
Polymers93,8964
Non-polymers2,0308
Water5,747319
1
A: ATP-dependent dethiobiotin synthetase BioD
B: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9636
Polymers46,9482
Non-polymers1,0154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-41 kcal/mol
Surface area17460 Å2
MethodPISA
2
C: ATP-dependent dethiobiotin synthetase BioD
D: ATP-dependent dethiobiotin synthetase BioD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9636
Polymers46,9482
Non-polymers1,0154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-40 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.680, 105.700, 153.260
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 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P9WPQ5, dethiobiotin synthase
#2: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.7 M NaCitrate, 0.1 M Imidazole pH 7.0 with 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→56.68 Å / Num. obs: 32594 / % possible obs: 99.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 41.77 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.432 / Rpim(I) all: 0.122 / Rrim(I) all: 0.449 / Net I/σ(I): 7.1 / Num. measured all: 428391 / Scaling rejects: 128
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.612.93.64635770.421.0413.79698.7
9.01-56.6811.20.0458060.9990.0130.04799.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CVE

6cve


Resolution: 2.5→49.963 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 33.58
RfactorNum. reflection% reflection
Rfree0.288 1639 5.05 %
Rwork0.2167 --
obs0.2203 32437 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.04 Å2 / Biso mean: 53.4035 Å2 / Biso min: 11.81 Å2
Refinement stepCycle: final / Resolution: 2.5→49.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6277 0 120 319 6716
Biso mean--30.87 38.65 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096556
X-RAY DIFFRACTIONf_angle_d1.3019008
X-RAY DIFFRACTIONf_chiral_restr0.0711124
X-RAY DIFFRACTIONf_plane_restr0.011175
X-RAY DIFFRACTIONf_dihedral_angle_d20.8883881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.57360.41091400.35192470261097
2.5736-2.65670.41031330.32982493262699
2.6567-2.75160.4041280.31462503263199
2.7516-2.86180.3561280.29332575270399
2.8618-2.9920.39551420.28392513265599
2.992-3.14970.35241170.274425772694100
3.1497-3.3470.32461600.257625242684100
3.347-3.60540.35521170.24725652682100
3.6054-3.96810.32091160.21926102726100
3.9681-4.54190.23251490.152425862735100
4.5419-5.72110.2141490.151526332782100
5.7211-49.97270.18531600.145127492909100
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)
11.8358-0.3913-0.05210.94390.54140.80260.08570.3448-0.2885-0.3595-0.0428-0.01960.221-0.0741-0.19880.661-0.0281-0.04710.31120.0080.3176-9.2761-31.817713.2299
21.8011-0.2140.46340.58010.32821.1345-0.15610.0919-0.1824-0.2461-0.05840.07140.5752-0.27870.20640.86580.0023-0.02630.3236-0.05080.3015-4.1521-38.288712.2628
31.53590.48740.12210.79040.33951.25910.16430.4059-0.1156-0.9306-0.1362-0.21050.40450.20060.05020.65740.00290.14130.45340.00250.241.4649-28.79487.4559
42.2691.86680.2336.2988-0.00984.20590.0032-0.363-0.2616-0.48270.1607-0.6408-0.43280.41050.31040.8066-0.0220.02040.26820.0910.18615.5901-24.735716.774
51.429-0.48280.00341.87850.29961.9453-0.1861-0.14610.1026-0.3279-0.025-0.01360.3463-0.05360.13560.47280.06410.01090.3683-0.01730.2428-8.2617-20.472422.3822
64.7156-0.244-0.31694.9003-1.58677.1941-0.45580.0911-0.55010.562-0.10080.0573-0.2094-0.14270.58110.46250.01810.03540.5974-0.01080.3642-17.9357-19.825932.6808
72.3122-0.14820.28923.0421-1.07922.5449-0.0057-0.0876-0.30210.29660.4370.6179-0.3501-0.8548-0.18330.53960.0488-0.0890.6567-0.0350.4365-21.4886-29.449516.6699
82.4516-0.6545-0.42380.96110.10421.90960.1907-0.19320.1521-0.2941-0.14580.06110.266-0.09560.01060.52770.0254-0.0540.2813-0.01460.26620.5011-14.807149.3729
91.4151-0.0325-0.29521.54350.29452.4520.02350.08310.0194-0.42310.0003-0.1360.1740.1997-0.06320.54240.1114-0.02240.3185-0.04060.25348.6487-20.884137.7923
101.3726-0.74130.62271.34380.65361.30910.2939-0.55410.52990.65710.06250.7452-0.0233-0.0748-0.37650.6256-0.04210.31620.3582-0.07730.6835-32.00734.736825.1468
110.20890.37880.06031.13-0.51740.78520.5799-0.3951-0.06761.6801-0.41040.1402-0.48620.0599-0.15170.8455-0.12050.25010.4385-0.13940.3583-19.25517.983429.4068
121.68030.20620.19711.26580.6841.76780.2003-0.06010.0950.43570.03840.3996-0.2642-0.0996-0.19620.4235-0.10340.14290.32970.03250.4399-28.90042.529918.1502
131.0112-0.41980.0960.1914-0.07670.10580.74090.24550.41890.06720.25320.3099-0.70020.08760.69510.78080.30941.26680.7051-0.08131.143-42.69446.922426.4342
141.74021.19050.68821.899-0.41640.99560.24180.13110.4359-0.1502-0.5375-0.31670.1299-0.0927-0.05460.32020.12720.1040.29640.00230.6062-16.23253.7541-7.2579
151.80611.42821.0083.4229-1.41912.6769-0.07650.3817-0.25650.2766-0.2128-0.6815-0.050.34390.53440.39990.08360.01820.49780.11230.3339-8.361310.448-12.1119
164.4797-1.0492-1.39942.66220.6273.01050.6360.41460.2108-0.3296-0.4165-0.365-0.59290.1903-0.03640.36760.10530.03380.39410.0630.348-21.002113.2466-13.5664
170.95160.94690.99192.4999-1.28164.45720.08940.22970.32560.7273-0.20680.3874-0.66550.22470.17810.3015-0.03390.10010.28330.03990.4566-14.950515.0642-16.8306
183.5888-0.4087-0.47741.2682-0.57362.81510.00740.0345-0.12570.06980.16420.3475-0.4822-0.2599-0.27170.56080.13120.03470.4164-0.01280.2544-34.591313.0148-10.0226
192.7644-0.51070.20792.6224-0.2513.53690.79670.3047-0.438-0.3154-0.4027-0.27550.98150.1566-0.06420.39330.055-0.00870.38130.01560.278-20.85250.7396-18.2744
201.9846-2.90280.98274.3746-2.36567.3713-0.0941-0.04970.2555-0.513-0.21820.06350.831-0.79830.15080.47290.00530.0530.3959-0.03320.3211-30.22962.9541-5.8449
210.9768-0.53990.14150.8437-0.3931.3548-0.2204-0.08180.1095-0.10170.15410.02910.31160.25070.08910.268-0.02390.02540.2885-0.01330.4195-18.30590.25130.9198
220.92130.49140.79332.84211.20431.68170.05440.18170.08450.65540.0121-0.6749-0.10.626-0.08850.3503-0.1267-0.00280.34640.04150.4565-8.91137.48211.9552
233.57240.53160.06343.10311.15621.02530.3797-0.1408-0.09850.37790.0293-0.28220.26630.38550.00740.155-0.0885-0.0620.7092-0.02640.545-5.95776.421610.729
242.2388-0.2051-0.94561.08340.52362.915-0.1115-0.18650.49130.08190.1737-0.3464-0.18720.9560.13220.3111-0.08990.02120.570.05940.5247-3.471410.1698-7.5181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 48 )A0 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 73 )A49 - 73
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 108 )A74 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 123 )A109 - 123
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 176 )A124 - 176
6X-RAY DIFFRACTION6chain 'A' and (resid 177 through 189 )A177 - 189
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 226 )A190 - 226
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 108 )B0 - 108
9X-RAY DIFFRACTION9chain 'B' and (resid 109 through 225 )B109 - 225
10X-RAY DIFFRACTION10chain 'C' and (resid -1 through 28 )C-1 - 28
11X-RAY DIFFRACTION11chain 'C' and (resid 29 through 87 )C29 - 87
12X-RAY DIFFRACTION12chain 'C' and (resid 88 through 204 )C88 - 204
13X-RAY DIFFRACTION13chain 'C' and (resid 205 through 226 )C205 - 226
14X-RAY DIFFRACTION14chain 'D' and (resid -1 through 14 )D-1 - 14
15X-RAY DIFFRACTION15chain 'D' and (resid 15 through 29 )D15 - 29
16X-RAY DIFFRACTION16chain 'D' and (resid 30 through 48 )D30 - 48
17X-RAY DIFFRACTION17chain 'D' and (resid 49 through 63 )D49 - 63
18X-RAY DIFFRACTION18chain 'D' and (resid 64 through 87 )D64 - 87
19X-RAY DIFFRACTION19chain 'D' and (resid 88 through 108 )D88 - 108
20X-RAY DIFFRACTION20chain 'D' and (resid 109 through 123 )D109 - 123
21X-RAY DIFFRACTION21chain 'D' and (resid 124 through 159 )D124 - 159
22X-RAY DIFFRACTION22chain 'D' and (resid 160 through 176 )D160 - 176
23X-RAY DIFFRACTION23chain 'D' and (resid 177 through 189 )D177 - 189
24X-RAY DIFFRACTION24chain 'D' and (resid 190 through 225 )D190 - 225

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