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- PDB-6d2s: Mycobacterium tuberculosis transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 6d2s
TitleMycobacterium tuberculosis transcriptional regulator
ComponentsHTH-type transcriptional regulator PrpR
KeywordsTRANSCRIPTION / Transcriptional regulator
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
HTH-type transcriptional regulator PrpR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.819 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 13, 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7568
Polymers32,4971
Non-polymers2597
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.999, 81.724, 95.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-501-

CA

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 32496.814 Da / Num. of mol.: 1 / Fragment: residues 155-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: prpR, Rv1129c, RVBD_1129c, P425_01178 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O06581

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Non-polymers , 5 types, 184 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: CaCl2, HEPES pH 7.5, PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 14, 2016
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 26651 / % possible obs: 99.8 % / Redundancy: 9.5 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.015 / Rrim(I) all: 0.045 / Χ2: 1.708 / Net I/σ(I): 20.5 / Num. measured all: 252505
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.82-1.857.30.24112740.9660.0950.261.50997.7
1.85-1.898.10.21313290.9770.080.2281.615100
1.89-1.928.60.18313270.9860.0670.1951.641100
1.92-1.969.40.1613030.9910.0560.1691.715100
1.96-29.90.14712880.9930.050.1551.855100
2-2.059.90.12913420.9940.0440.1361.826100
2.05-2.19.90.10913320.9960.0370.1161.837100
2.1-2.169.90.09513150.9960.0320.11.861100
2.16-2.229.90.08213400.9970.0280.0871.798100
2.22-2.299.90.07313080.9980.0240.0771.842100
2.29-2.379.90.06613120.9980.0220.071.762100
2.37-2.479.90.0613320.9980.020.0641.734100
2.47-2.589.80.05513280.9990.0190.0581.721100
2.58-2.729.90.04813340.9990.0160.051.665100
2.72-2.899.80.04213290.9990.0140.0451.664100
2.89-3.119.80.03713470.9990.0120.0391.621100
3.11-3.439.80.031134710.010.0331.559100
3.43-3.929.70.028136410.0090.0291.584100
3.92-4.949.50.025136910.0080.0271.507100
4.94-508.60.0314310.9990.0110.0331.76499

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Processing

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

6cz6


Resolution: 1.819→32.095 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1343 5.04 %Random selection
Rwork0.1765 25305 --
obs0.1781 26648 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.68 Å2 / Biso mean: 28.1263 Å2 / Biso min: 8.51 Å2
Refinement stepCycle: final / Resolution: 1.819→32.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 16 177 2381
Biso mean--32.44 36.18 -
Num. residues----275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.819-1.8840.26521330.20042475260899
1.884-1.95940.27131290.18624992628100
1.9594-2.04860.21851420.182724882630100
2.0486-2.15660.22511630.168624822645100
2.1566-2.29170.2191380.166325052643100
2.2917-2.46850.19721170.166225312648100
2.4685-2.71690.21991210.172525382659100
2.7169-3.10970.20131170.179725602677100
3.1097-3.91680.17041340.168125742708100
3.9168-32.09960.21471490.185226532802100
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)
11.40730.0386-0.4961.4003-0.79180.976-0.01080.00470.1066-0.04140.0219-0.04560.0114-0.0098-0.00420.1118-0.0038-0.00820.0831-0.00360.1-27.4846-16.4805-20.7024
21.8751-0.72270.54022.22-0.75872.2845-0.0418-0.54620.22080.1194-0.0707-0.2296-0.32050.27890.12740.1817-0.01520.00570.38430.05880.2249-18.3158-27.4552-4.1999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 153 through 333 )A153 - 333
2X-RAY DIFFRACTION2chain 'A' and (resid 334 through 436 )A334 - 436

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