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- PDB-5cxg: Crystal structure of Mycobacterium tuberculosis KstR in complex w... -

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Basic information

Entry
Database: PDB / ID: 5cxg
TitleCrystal structure of Mycobacterium tuberculosis KstR in complex with PEG
ComponentsHTH-type transcriptional repressor KstR
KeywordsTranscription regulator / Transcriptional repressor / TetR family Transcriptional repressor / cholesterol catabolism / CoA thioester ligand / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding
Similarity search - Function
HTH-type transcriptional repressor KstR, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / HTH-type transcriptional repressor KstR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1001 Å
AuthorsHo, N.A.T. / Dawes, S. / Kendall, S. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC)
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC)12/1111 New Zealand
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Structure of the Transcriptional Repressor KstR in Complex with CoA Thioester Cholesterol Metabolites Sheds Light on the Regulation of Cholesterol Catabolism in Mycobacterium tuberculosis.
Authors: Ho, N.A. / Dawes, S.S. / Crowe, A.M. / Casabon, I. / Gao, C. / Kendall, S.L. / Baker, E.N. / Eltis, L.D. / Lott, J.S.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: HTH-type transcriptional repressor KstR
B: HTH-type transcriptional repressor KstR
C: HTH-type transcriptional repressor KstR
D: HTH-type transcriptional repressor KstR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9678
Polymers89,4104
Non-polymers5574
Water3,747208
1
A: HTH-type transcriptional repressor KstR
B: HTH-type transcriptional repressor KstR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0054
Polymers44,7052
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-9 kcal/mol
Surface area15760 Å2
MethodPISA
2
C: HTH-type transcriptional repressor KstR
D: HTH-type transcriptional repressor KstR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9614
Polymers44,7052
Non-polymers2562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-9 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.030, 38.380, 154.718
Angle α, β, γ (deg.)90.00, 111.69, 90.00
Int Tables number5
Space group name H-MI121
DetailsDimer confirmed by SEC-MALLS

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Components

#1: Protein
HTH-type transcriptional repressor KstR


Mass: 22352.510 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: kstR, Rv3574 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P96856
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 8% PEG 3350, 25% PEG 400, 0.1 M magnesium chloride, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1001→37.41 Å / Num. obs: 40309 / % possible obs: 98.5 % / Redundancy: 3.6 % / Net I/σ(I): 4.6
Reflection shellResolution: 2.1001→2.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 1.4 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MNL

3mnl


Resolution: 2.1001→37.409 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 1991 4.94 %
Rwork0.2098 --
obs0.2122 40302 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1001→37.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 31 208 5368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125631
X-RAY DIFFRACTIONf_angle_d0.6557106
X-RAY DIFFRACTIONf_dihedral_angle_d12.2341751
X-RAY DIFFRACTIONf_chiral_restr0.03867
X-RAY DIFFRACTIONf_plane_restr0.003911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.15260.31651350.28122607X-RAY DIFFRACTION94
2.1526-2.21080.38831480.26592618X-RAY DIFFRACTION96
2.2108-2.27580.29091310.25932707X-RAY DIFFRACTION97
2.2758-2.34930.28171360.23842644X-RAY DIFFRACTION97
2.3493-2.43320.28241460.23342689X-RAY DIFFRACTION99
2.4332-2.53060.29711480.22132752X-RAY DIFFRACTION100
2.5306-2.64570.27851460.23212707X-RAY DIFFRACTION99
2.6457-2.78520.27831190.2142774X-RAY DIFFRACTION100
2.7852-2.95960.26531380.22512804X-RAY DIFFRACTION100
2.9596-3.1880.25821500.22862766X-RAY DIFFRACTION100
3.188-3.50860.29191300.20312756X-RAY DIFFRACTION99
3.5086-4.01580.21191580.18312739X-RAY DIFFRACTION99
4.0158-5.05760.22221600.17222820X-RAY DIFFRACTION100
5.0576-37.41480.23981460.20032928X-RAY DIFFRACTION100
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)
11.7853-0.19250.54930.1588-0.1310.2042-0.0083-0.0631-0.0243-0.03170.07130.01930.0848-0.1601-0.05810.1293-0.0629-0.17971.51380.49170.6236-57.54049.3273-17.532
20.03730.1018-0.06450.2787-0.17790.11350.15730.261-0.2188-0.00040.0765-0.05610.14720.0892-0.00550.2681-0.2498-0.20810.87180.15570.2694-54.65818.8402-27.1611
31.97580.36590.60490.91290.69270.5858-0.0409-0.44020.17860.3420.23420.4164-0.0192-1.0659-0.64390.23330.06920.03771.32960.24010.4908-50.617611.6233-13.7347
45.2944-1.9066-1.97545.1671-0.04051.42770.3670.7432-0.27590.1505-0.29390.3780.9857-1.1406-0.15480.4925-0.107-0.0130.65740.10820.2728-38.0212-3.221-8.2825
52.49912.213-1.08697.15810.51693.5454-0.15260.82730.3891-0.6549-0.03570.7070.1141-0.78940.22870.3044-0.0658-0.09630.84640.13090.3781-46.03156.8661-23.577
60.14321.1395-0.58479.2609-5.16453.3230.0999-0.37540.0795-0.00580.17640.6335-0.1649-0.6171-0.3120.26740.04880.0470.56190.03460.2187-38.010812.3706-12.4791
72.6298-0.573-0.86042.4363-0.65410.58770.1413-0.388-0.17730.49620.0755-0.16280.4203-0.5554-0.16310.21-0.0283-0.00950.23370.07610.1822-32.25994.3827-12.2532
80.87180.0702-0.87931.3292-0.45550.99080.1236-0.1705-0.48860.11870.08920.04320.7663-0.3915-0.11830.4038-0.1045-0.07160.24820.11880.2742-31.346-6.4739-16.6357
98.8626-2.21321.82915.6052-4.53574.8424-0.55020.860.0107-0.22460.1243-0.27110.02020.38980.23890.3232-0.146-0.07540.37930.04740.2267-31.56659.4011-49.4686
100.12090.00410.78170.6114-0.27697.0179-0.08610.31090.4434-0.21490.22670.2328-0.5289-0.2157-0.02990.4093-0.0704-0.13480.33350.09330.287-40.891312.5847-48.0815
113.62561.4438-2.49119.1576-4.88843.48290.12720.7435-0.278-0.41030.3061-0.09840.9389-1.3789-0.32240.431-0.1901-0.00870.5012-0.0810.3704-39.34783.3019-52.5308
126.78990.0930.05490.970.12272.9385-0.0786-0.0162-0.0697-0.2725-0.0576-0.08630.25050.22390.13160.2062-0.01930.00940.09010.05070.1635-28.64865.408-40.5717
130.0041-0.0792-0.08162.53151.62793.38280.3351-0.08610.3134-0.01990.3743-0.61790.0230.8097-0.02960.3918-0.15610.21380.3306-0.37760.602-14.10578.4044-28.8972
146.0313.0188-0.41445.8148-1.28528.769-0.2222-0.2090.4657-0.33160.0340.4592-0.582-0.83650.06220.29940.0766-0.07990.3255-0.01380.2371-35.069110.5749-34.1221
155.14312.71321.86791.5181.35722.73920.2583-0.0128-0.4191-0.0753-0.05550.15310.39840.1908-0.14610.1793-0.0277-0.04150.04710.01070.2301-25.4481-1.5054-32.1423
166.7885-5.1922-0.6564.23590.70940.89110.0013-0.1214-0.0848-0.11940.0488-0.12170.0145-0.0222-0.05460.1787-0.0283-0.01240.16050.0180.1479-23.95842.0866-24.5971
178.70184.44870.50963.51080.96827.0503-0.07790.24350.8461-0.08320.54020.5142-1.0661-0.6839-0.3410.32140.10880.00640.29770.01330.2626-33.313319.6849-23.0045
180.71651.6164-1.24545.2606-1.72122.925-0.2064-0.20410.36540.999-0.0134-0.7182-0.50110.37670.07980.2508-0.0341-0.07320.162-0.01220.2709-20.784410.738-17.4321
193.8545-2.0671.28355.266-0.92543.3958-0.30520.4458-0.0589-0.36050.3340.1192-0.04480.38790.01080.4067-0.1231-0.07540.60450.11190.3216-45.9692-17.3532-66.2543
207.2448-1.22221.92797.3687-0.91118.0475-0.13241.21470.1099-1.13930.0792-0.0254-0.39081.4310.07270.502-0.0826-0.0370.52710.0580.2329-48.09-15.7447-73.7787
212.8283-1.6147-0.25933.36130.49793.629-0.0475-0.0422-0.1832-0.006-0.20880.15790.0311-0.64850.27340.3477-0.1105-0.09450.41590.07280.2489-50.5897-19.645-62.024
225.5317-0.1483-5.61833.2574-2.59248.124-0.039-0.7194-0.0405-0.01670.4155-0.01680.40550.38890.00730.66630.0446-0.24880.36440.05780.3865-40.9631-13.8124-36.1612
234.5544.1891-4.55734.3692-4.58644.8884-0.36690.53990.1814-0.05920.1759-0.1219-0.6956-0.66950.18880.51890.007-0.13660.34740.06270.3557-48.8173-9.4278-41.4245
247.09863.752-1.79657.578-0.19858.5745-0.21640.76880.4627-0.95870.06570.0685-0.20860.06880.19950.3589-0.0218-0.04430.47060.16390.3505-56.676-10.4353-59.2257
259.29290.08247.97443.22380.76118.20660.11140.34660.2556-0.0485-0.1876-0.12231.0085-0.06180.01720.4083-0.113-0.06410.33410.10290.2678-56.6802-21.8174-51.3487
267.0901-4.58852.61226.9194-1.1064.1620.0665-0.10360.2170.3163-0.0143-0.27290.4019-0.3774-0.10620.372-0.1094-0.05160.48370.04850.2433-56.6284-15.9774-41.9845
278.4155.97986.20474.84612.91788.99380.6468-0.4624-0.53190.6316-0.35250.07311.668-0.6159-0.3970.98790.16390.04810.51460.01290.4545-60.73441.8468-51.6052
287.1173-2.51531.87087.7155-3.17851.445-0.0317-1.07580.3441.3187-0.3179-0.6034-1.1546-0.12940.37050.5480.0027-0.09110.4653-0.03740.3229-58.032-5.4766-37.6705
297.4959-2.2221-2.88363.24771.96564.48740.4739-0.60440.56910.17130.1331-0.0323-0.0282-0.2605-0.5390.54540.00430.00790.91760.19540.4987-82.7515-5.5562-67.5723
303.5113-3.36051.72935.3171-0.02262.22830.1971-0.33220.36230.0638-0.484-0.29520.0740.53710.25330.3963-0.0320.00250.99190.24560.6208-79.6604-1.6187-59.1935
310.26180.1386-0.25180.31190.03220.35820.4051-0.20710.1778-0.1636-0.2969-0.1588-0.20.0469-0.05090.9838-0.02170.29791.93230.1920.6897-86.0772-12.2947-34.8637
320.817-0.3623-2.01510.67160.40545.52880.20780.1266-0.16220.1057-0.5298-0.13350.3404-0.77850.30120.5528-0.1186-0.04871.19550.18720.4111-75.9347-13.5652-49.775
333.6276-1.4351-1.24377.20381.52013.50220.21530.06870.6130.31940.01660.0567-0.1088-0.8767-0.17840.4292-0.05050.05060.94310.08290.3949-71.0441-9.3275-45.2676
345.28232.23363.17677.8638-1.1298.5992-0.41280.3498-0.52390.04350.66690.00990.1556-0.595-0.01420.5295-0.2610.02170.86320.090.3079-69.6744-20.742-40.0215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 88 )
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 122 )
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 143 )
7X-RAY DIFFRACTION7chain 'A' and (resid 144 through 172 )
8X-RAY DIFFRACTION8chain 'A' and (resid 173 through 196 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 32 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 46 )
11X-RAY DIFFRACTION11chain 'B' and (resid 47 through 59 )
12X-RAY DIFFRACTION12chain 'B' and (resid 60 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 104 )
14X-RAY DIFFRACTION14chain 'B' and (resid 105 through 122 )
15X-RAY DIFFRACTION15chain 'B' and (resid 123 through 145 )
16X-RAY DIFFRACTION16chain 'B' and (resid 146 through 172 )
17X-RAY DIFFRACTION17chain 'B' and (resid 173 through 177 )
18X-RAY DIFFRACTION18chain 'B' and (resid 178 through 194 )
19X-RAY DIFFRACTION19chain 'C' and (resid 12 through 36 )
20X-RAY DIFFRACTION20chain 'C' and (resid 37 through 49 )
21X-RAY DIFFRACTION21chain 'C' and (resid 50 through 78 )
22X-RAY DIFFRACTION22chain 'C' and (resid 79 through 88 )
23X-RAY DIFFRACTION23chain 'C' and (resid 89 through 106 )
24X-RAY DIFFRACTION24chain 'C' and (resid 107 through 122 )
25X-RAY DIFFRACTION25chain 'C' and (resid 123 through 141 )
26X-RAY DIFFRACTION26chain 'C' and (resid 142 through 172 )
27X-RAY DIFFRACTION27chain 'C' and (resid 173 through 177 )
28X-RAY DIFFRACTION28chain 'C' and (resid 178 through 193 )
29X-RAY DIFFRACTION29chain 'D' and (resid 14 through 49 )
30X-RAY DIFFRACTION30chain 'D' and (resid 50 through 77 )
31X-RAY DIFFRACTION31chain 'D' and (resid 78 through 88 )
32X-RAY DIFFRACTION32chain 'D' and (resid 89 through 122 )
33X-RAY DIFFRACTION33chain 'D' and (resid 123 through 177 )
34X-RAY DIFFRACTION34chain 'D' and (resid 178 through 193 )

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