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- PDB-6cyy: Mycobacterium tuberculosis transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 6cyy
TitleMycobacterium tuberculosis transcriptional regulator
ComponentsHTH-type transcriptional regulator PrpR
KeywordsTRANSCRIPTION / 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
COENZYME A / IRON/SULFUR CLUSTER / HTH-type transcriptional regulator PrpR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 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 7, 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 1.2Oct 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)97,5866
Polymers95,3472
Non-polymers2,2384
Water724
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)195,17112
Polymers190,6954
Non-polymers4,4778
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area23610 Å2
ΔGint-152 kcal/mol
Surface area49710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.871, 144.871, 97.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
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 - 481 / Label seq-ID: 95 - 424

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: 47673.641 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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: Bicine pH9.5, Sodium Acetate, Zwittergent 3-14

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2017
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 35534 / % possible obs: 98.4 % / Redundancy: 21.2 % / Biso Wilson estimate: 70.26 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.013 / Rrim(I) all: 0.061 / Χ2: 1.029 / Net I/σ(I): 9.2 / Num. measured all: 753694
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5422.60.73317730.9670.1570.750.393100
2.54-2.5922.30.56517670.980.1210.5780.406100
2.59-2.6422.30.47317800.9820.1020.4840.416100
2.64-2.6921.80.38817710.9880.0840.3970.43299.9
2.69-2.7521.30.31517740.9910.0690.3230.457100
2.75-2.8219.40.25417730.9930.0590.2610.484100
2.82-2.8922.40.20817750.9960.0450.2130.505100
2.89-2.9622.70.1717880.9970.0360.1740.558100
2.96-3.0522.60.13517810.9980.0290.1380.636100
3.05-3.1522.10.11317990.9980.0240.1150.744100
3.15-3.2621.70.09517750.9990.0210.0970.869100
3.26-3.3920.60.08417860.9990.0190.0861.094100
3.39-3.5520.60.07718120.9990.0170.0791.195100
3.55-3.7318.30.0712370.9990.0160.0721.25868.5
3.73-3.9719.90.06618010.9990.0150.0681.66399.5
3.97-4.2721.50.05518160.9990.0120.0571.81399.8
4.27-4.719.90.05218250.9990.0120.0531.90899.7
4.7-5.3822.10.04918420.9990.010.051.87399.9
5.38-6.7819.90.04818610.9990.0110.0491.882100
6.78-5019.60.04119980.9990.0090.0422.23199.9

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Processing

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

6cz6


Resolution: 2.506→46.104 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 1997 5.63 %Random selection
Rwork0.1835 33471 --
obs0.1852 35468 98.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.77 Å2 / Biso mean: 77.7527 Å2 / Biso min: 48.01 Å2
Refinement stepCycle: final / Resolution: 2.506→46.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5172 0 112 4 5288
Biso mean--73.98 62.62 -
Num. residues----660
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2034X-RAY DIFFRACTION4.889TORSIONAL
12B2034X-RAY DIFFRACTION4.889TORSIONAL
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 (%)
2.5056-2.56820.30911400.26292357249799
2.5682-2.63770.28911430.247623942537100
2.6377-2.71530.30351410.245823682509100
2.7153-2.80290.32641450.242224082553100
2.8029-2.90310.32231430.250624042547100
2.9031-3.01930.28761440.26724082552100
3.0193-3.15660.31811430.25324002543100
3.1566-3.3230.28961440.239524112555100
3.323-3.53120.26951450.225324242569100
3.5312-3.80370.22611130.20411892200578
3.8037-4.18620.18571440.15992433257799
4.1862-4.79140.16671470.137124452592100
4.7914-6.03460.17541500.157625072657100
6.0346-46.11190.17141550.153926202775100
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)
13.87581.0319-1.60913.2519-0.68835.0630.2309-0.38490.38930.4813-0.29460.6428-0.96950.12360.15550.65070.023-0.05580.7062-0.12120.6294-23.732165.0271-5.3297
26.48990.84283.52313.96880.48834.08590.20620.61950.43120.1284-0.15550.1968-0.20340.06970.08780.804-0.01360.00130.75310.05230.7838-10.912369.6604-23.3174
33.79481.2213-0.06553.1845-0.22052.7680.1087-0.383-0.49160.0123-0.1114-0.47220.10240.4823-0.00110.57060.0066-0.02480.73630.07640.6187-4.344755.3132-18.8086
43.94030.31820.53021.10470.0321.6065-0.0336-0.4440.39460.2131-0.10520.1697-0.2634-0.12420.190.61150.0521-0.00690.5266-0.07420.6515-23.783264.0517-13.1687
54.17141.3810.73724.0465-1.46942.53710.2744-0.4637-0.09150.3731-0.22620.59340.2051-0.2631-0.00640.59340.0566-0.02670.6937-0.08630.6892-37.194248.4163-10.2251
61.1721-1.22630.01865.05151.74440.9276-0.6761-0.797-0.11040.09480.48340.49830.40050.3820.05580.78820.1115-0.02340.68850.03490.5716-27.834844.7759-18.5721
70.94381.71650.34573.4622-0.23132.18130.02010.20630.1290.2691-0.14540.87890.04-0.17940.09160.61960.11590.08060.651-0.08020.8969-45.080154.2609-16.3542
87.01830.2751.176.9307-0.76280.45250.2781-0.7475-0.07690.8307-0.32090.7153-0.0216-0.781-0.08950.93720.00860.1660.9895-0.05120.9671-46.556239.12150.4077
94.03651.48760.36792.1599-0.1830.17260.6399-0.92260.82191.0207-0.60570.6696-0.66110.5637-0.25011.1724-0.17740.12471.3306-0.14040.7867-53.753528.94863.4963
103.07330.2688-0.22871.3751-0.12012.24520.0815-0.4674-0.41160.2646-0.1947-0.10170.1955-0.04110.08840.67320.0130.00090.67030.1380.6318-47.89213.238-2.0965
114.20750.7874-0.53175.585-0.05622.35480.179-0.9389-0.42950.9054-0.1075-0.5025-0.02410.2301-0.00850.59690.0678-0.0620.7180.130.6413-33.155626.5994-2.6428
123.80092.2982-1.74215.15221.24342.45880.09-0.16230.12750.0637-0.41-0.7502-0.05780.23050.16380.59060.09240.03580.6890.16070.72-28.022427.4152-12.9249
130.51221.0062-0.30682.6567-0.94311.8177-0.3136-0.6527-0.257-0.07050.3467-0.13310.0874-0.2299-0.15960.56030.1096-0.11110.7117-0.01820.5484-39.251725.8664-12.9875
141.72461.30090.17763.29920.81470.24950.0294-0.2031-0.115-0.1723-0.1467-0.6293-0.31680.53510.06360.65930.0669-0.06330.86070.23920.8632-19.145330.5921-9.9976
150.7383-0.209-0.85320.06160.21521.11740.7111-1.3388-1.08520.996-0.4409-0.77670.3535-0.2292-0.13711.1423-0.2319-0.17531.41070.17561.1003-11.305849.6208-5.7139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 152 through 182 )A152 - 182
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 202 )A183 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 234 )A203 - 234
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 334 )A235 - 334
5X-RAY DIFFRACTION5chain 'A' and (resid 335 through 389 )A335 - 389
6X-RAY DIFFRACTION6chain 'A' and (resid 390 through 410 )A390 - 410
7X-RAY DIFFRACTION7chain 'A' and (resid 411 through 444 )A411 - 444
8X-RAY DIFFRACTION8chain 'A' and (resid 445 through 464 )A445 - 464
9X-RAY DIFFRACTION9chain 'A' and (resid 465 through 481 )A465 - 481
10X-RAY DIFFRACTION10chain 'B' and (resid 152 through 334 )B152 - 334
11X-RAY DIFFRACTION11chain 'B' and (resid 335 through 360 )B335 - 360
12X-RAY DIFFRACTION12chain 'B' and (resid 361 through 398 )B361 - 398
13X-RAY DIFFRACTION13chain 'B' and (resid 399 through 425 )B399 - 425
14X-RAY DIFFRACTION14chain 'B' and (resid 426 through 464 )B426 - 464
15X-RAY DIFFRACTION15chain 'B' and (resid 465 through 481 )B465 - 481

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