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- PDB-6cyj: Mycobacterium tuberculosis transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 6cyj
TitleMycobacterium tuberculosis transcriptional regulator
ComponentsHTH-type transcriptional regulator PrpR
KeywordsTRANSCRIPTION / Transcriptional Regulator / DNA BINDING PROTEIN
Function / homology
Function and homology information


propionate metabolic process, methylcitrate cycle / response to host immune response / cholesterol metabolic process / response to hypoxia / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
Short-chain fatty acyl coenzyme A regulators, C-terminal / HTH-type transcriptional regulator RamB / Short-chain fatty acyl coenzyme A regulators / IrrE N-terminal-like domain / IrrE N-terminal-like domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
SUCCINYL-COENZYME A / IRON/SULFUR CLUSTER / HTH-type transcriptional regulator PrpR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å
AuthorsTang, S. / Sacchettini, J.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor.
Authors: Tang, S. / Hicks, N.D. / Cheng, Y.S. / Silva, A. / Fortune, S.M. / Sacchettini, J.C.
History
DepositionApr 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Oct 4, 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: HTH-type transcriptional regulator PrpR
B: HTH-type transcriptional regulator PrpR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7686
Polymers95,3292
Non-polymers2,4384
Water362
1
A: HTH-type transcriptional regulator PrpR
B: HTH-type transcriptional regulator PrpR
hetero molecules

A: HTH-type transcriptional regulator PrpR
B: HTH-type transcriptional regulator PrpR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,53512
Polymers190,6584
Non-polymers4,8778
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area24410 Å2
ΔGint-208 kcal/mol
Surface area49650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.485, 144.485, 96.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 152 - 480 / Label seq-ID: 95 - 423

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein HTH-type transcriptional regulator PrpR / Propionate regulator / PRPR


Mass: 47664.613 Da / Num. of mol.: 2 / Fragment: residues 81-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: prpR, Rv1129c, RVBD_1129c, P425_01178 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O06581
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SCA / SUCCINYL-COENZYME A


Mass: 867.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O19P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: Bicine pH9.5, Sodium Acetate, Zwittergent 3-14 / PH range: 7.5-9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 27986 / % possible obs: 97.8 % / Redundancy: 17 % / Biso Wilson estimate: 78.74 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.019 / Rrim(I) all: 0.08 / Χ2: 1.123 / Net I/σ(I): 7.7 / Num. measured all: 475646
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.7517.11.05214140.9280.2581.0830.458100
2.75-2.817.40.8613850.9460.210.8850.449100
2.8-2.8517.40.72314100.9570.1770.7450.46100
2.85-2.9116.80.58114040.9740.1440.5990.468100
2.91-2.9716.60.47913970.9860.120.4950.491100
2.97-3.0416.90.35914090.9860.0890.370.526100
3.04-3.12180.30214020.9890.0720.310.551100
3.12-3.218.10.2314180.9940.0550.2370.599100
3.2-3.317.90.18314110.9950.0440.1880.714100
3.3-3.417.60.15314020.9960.0370.1580.836100
3.4-3.5217.10.14114260.9970.0350.1450.937100
3.52-3.6615.30.13411850.9970.0340.1381.14684
3.66-3.8316.50.10610780.9970.0260.111.24275.2
3.83-4.03170.09714260.9970.0240.11.72799.4
4.03-4.2917.50.07914110.9980.0190.0811.92699.4
4.29-4.6216.80.07214360.9980.0180.0742.08199.2
4.62-5.0816.20.06614380.9980.0170.0682.09199.6
5.08-5.8117.70.0614570.9990.0140.0621.86599.8
5.81-7.3216.20.05414880.9990.0140.0561.902100
7.32-5015.70.04415890.9990.0110.0452.03899.7

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Processing

Software
NameVersionClassification
PHENIX1.13rc1_2954refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CZ6

6cz6


Resolution: 2.699→45.69 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 1998 7.16 %
Rwork0.1845 25897 -
obs0.187 27895 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.14 Å2 / Biso mean: 86.1711 Å2 / Biso min: 55.26 Å2
Refinement stepCycle: final / Resolution: 2.699→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5158 0 196 2 5356
Biso mean--89.4 69.6 -
Num. residues----658
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3147X-RAY DIFFRACTION6.667TORSIONAL
12B3147X-RAY DIFFRACTION6.667TORSIONAL
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 (%)
2.6991-2.76660.38011440.287618602004100
2.7666-2.84130.33681420.263418491991100
2.8413-2.92490.27191440.254718632007100
2.9249-3.01930.30231440.255618712015100
3.0193-3.12720.25231420.236918451987100
3.1272-3.25240.30781440.226918622006100
3.2524-3.40040.31381450.235318772022100
3.4004-3.57960.27681460.223918892035100
3.5796-3.80380.25451040.21791334143871
3.8038-4.09730.24311430.18671856199999
4.0973-4.50930.20251460.15581891203799
4.5093-5.1610.16211460.147219082054100
5.161-6.49930.19231510.169919422093100
6.4993-45.69670.17061570.155620502207100
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)
12.2272-0.34340.59432.1366-0.20241.91660.0747-0.15370.3844-0.0892-0.0960.1596-0.5406-0.0984-0.15870.8543-0.0183-0.03680.7814-0.13950.8992-18.957966.5995-11.7273
22.97240.4103-0.23161.2456-0.22221.87690.0309-0.23290.21460.1168-0.15740.0844-0.24720.120.09510.73530.0239-0.02860.6964-0.06180.8432-18.908461.7396-14.4014
33.63820.35520.51122.9186-0.95671.38580.275-0.4319-0.02530.4918-0.22120.59220.1469-0.24290.1110.73240.0932-0.01390.8474-0.0860.9023-37.084248.3835-9.8502
40.8231-0.52460.75793.85731.0081.2329-0.2289-0.58610.1163-0.35890.44530.1450.37460.68440.0840.91170.1526-0.0090.84630.00410.9022-27.763844.8277-18.3998
51.29111.9591-0.48153.001-1.18772.22540.01720.3470.18740.0202-0.05220.9945-0.1078-0.2476-0.09750.75160.1119-0.00290.9013-0.16621.2185-44.877853.8173-15.4709
62.02362.4227-0.04522.88560.00370.07040.3169-0.75440.29220.4989-0.28930.00630.0466-0.43150.11421.1343-0.05450.14411.2875-0.20861.1578-49.778434.36582.1607
72.44960.86791.02533.16721.18772.28480.2578-0.6609-0.48720.6001-0.2788-0.36670.05750.1881-0.01721.0130.0235-0.0381.24150.2070.9365-40.689513.68585.16
83.45481.0419-0.18052.71310.22683.1721-0.0193-0.2554-0.0830.2702-0.07220.43470.2583-0.4120.10390.8561-0.02440.04811.03250.05020.9102-61.365714.3228-5.2486
92.44951.10790.05762.0404-0.96332.33760.2848-0.8544-0.07780.3215-0.3719-0.09-0.0091-0.2382-0.24220.7258-0.03420.00140.93420.12880.7477-49.768414.66875.5927
104.11620.075-1.38321.64540.57472.7384-0.0541-0.5443-0.70880.3086-0.1328-0.18590.4360.32040.17020.76920.0359-0.02630.73240.14570.8862-39.939711.4505-5.7482
112.94981.3386-0.68173.942-0.48841.4889-0.0047-0.9425-0.11640.9926-0.0865-0.551-0.5090.47410.12960.8810.0789-0.07561.01430.10160.9191-32.966626.5874-2.279
122.68031.0721-1.33363.06070.46091.01830.1438-0.1252-0.10650.0764-0.2361-0.6202-0.13950.4591-0.07940.74670.1002-0.00980.85740.10330.9581-27.232228.5991-12.8447
130.07370.1549-0.2963.2429-1.19361.5435-0.1614-0.58780.1201-0.4895-0.0928-0.0863-0.2513-0.68850.0630.83330.1974-0.11031.0152-0.05991.0169-41.339629.0452-13.9862
140.81691.3146-0.18832.37660.24761.2977-0.1552-0.22620.1382-0.01650.1043-0.5946-0.11650.32410.08760.72890.1701-0.00170.90430.14720.9734-23.791220.5068-13.6594
151.69232.2019-0.85872.8719-1.3140.71330.2614-0.5422-0.22270.4514-0.3434-0.5702-0.27550.19280.14831.0942-0.1249-0.09781.37320.1571.1303-15.087144.2239-4.4287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 152 through 202 )A152 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 334 )A203 - 334
3X-RAY DIFFRACTION3chain 'A' and (resid 335 through 389 )A335 - 389
4X-RAY DIFFRACTION4chain 'A' and (resid 390 through 410 )A390 - 410
5X-RAY DIFFRACTION5chain 'A' and (resid 411 through 446 )A411 - 446
6X-RAY DIFFRACTION6chain 'A' and (resid 447 through 480 )A447 - 480
7X-RAY DIFFRACTION7chain 'B' and (resid 152 through 182 )B152 - 182
8X-RAY DIFFRACTION8chain 'B' and (resid 183 through 234 )B183 - 234
9X-RAY DIFFRACTION9chain 'B' and (resid 235 through 266 )B235 - 266
10X-RAY DIFFRACTION10chain 'B' and (resid 267 through 334 )B267 - 334
11X-RAY DIFFRACTION11chain 'B' and (resid 335 through 360 )B335 - 360
12X-RAY DIFFRACTION12chain 'B' and (resid 361 through 389 )B361 - 389
13X-RAY DIFFRACTION13chain 'B' and (resid 390 through 410 )B390 - 410
14X-RAY DIFFRACTION14chain 'B' and (resid 411 through 446 )B411 - 446
15X-RAY DIFFRACTION15chain 'B' and (resid 447 through 480 )B447 - 480

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