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- PDB-4fx4: Crystal structure of M. tuberculosis transcriptional regulator MO... -

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Basic information

Entry
Database: PDB / ID: 4fx4
TitleCrystal structure of M. tuberculosis transcriptional regulator MOSR (Rv1049) in compex with DNA
Components
  • DNA (5'-D(*TP*AP*CP*AP*GP*AP*TP*TP*CP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*GP*AP*AP*TP*CP*TP*GP*T)-3')
  • PROBABLE TRANSCRIPTIONAL REPRESSOR PROTEIN
KeywordsTRANSCRIPTION REGULATOR/DNA / Helix-turn-helix / Transcriptional repressor / DNA binding / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / cytosol
Similarity search - Function
MarR family / : / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Transcriptional regulator, MarR family, putative
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1001 Å
AuthorsBrugarolas, P. / He, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Oxidation-sensing Regulator (MosR) Is a New Redox-dependent Transcription Factor in Mycobacterium tuberculosis.
Authors: Brugarolas, P. / Movahedzadeh, F. / Wang, Y. / Zhang, N. / Bartek, I.L. / Gao, Y.N. / Voskuil, M.I. / Franzblau, S.G. / He, C.
History
DepositionJul 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*TP*AP*CP*AP*GP*AP*TP*TP*CP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*GP*AP*AP*TP*CP*TP*GP*T)-3')
C: DNA (5'-D(*TP*AP*CP*AP*GP*AP*TP*TP*CP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*GP*AP*AP*TP*CP*TP*GP*T)-3')
A: PROBABLE TRANSCRIPTIONAL REPRESSOR PROTEIN
B: PROBABLE TRANSCRIPTIONAL REPRESSOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5995
Polymers50,5044
Non-polymers951
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11620 Å2
ΔGint-87 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.585, 146.585, 53.887
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: DNA chain DNA (5'-D(*TP*AP*CP*AP*GP*AP*TP*TP*CP*GP*TP*GP*TP*AP*GP*CP*TP*AP*CP*AP*CP*GP*AP*AP*TP*CP*TP*GP*T)-3')


Mass: 8908.758 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic DNA corresponding to the promoter sequence of Rv1049
Source: (synth.) Synthetic DNA (others)
#2: Protein PROBABLE TRANSCRIPTIONAL REPRESSOR PROTEIN / Transcriptional regulator / MarR family / putative


Mass: 16343.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1079, Rv1049 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O53397
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.4 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2011
RadiationMonochromator: CRYO-COOLED DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→29.475 Å / Num. all: 7828 / Num. obs: 7799 / % possible obs: 99.62 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.1→3.31 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z9C

1z9c


Resolution: 3.1001→29.475 Å / SU ML: 0.42 / σ(F): 2 / Phase error: 33.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 360 4.62 %
Rwork0.2401 --
obs0.2419 7799 99.62 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.3 Å2 / ksol: 0.305 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.4923 Å20 Å20 Å2
2---13.4923 Å2-0 Å2
3---26.9847 Å2
Refinement stepCycle: LAST / Resolution: 3.1001→29.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 964 5 0 2965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033094
X-RAY DIFFRACTIONf_angle_d0.8184373
X-RAY DIFFRACTIONf_dihedral_angle_d22.3771227
X-RAY DIFFRACTIONf_chiral_restr0.045508
X-RAY DIFFRACTIONf_plane_restr0.003396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.5480.3241220.2992470X-RAY DIFFRACTION99
3.548-4.46760.31271090.24622487X-RAY DIFFRACTION100
4.4676-29.47610.25161290.22012482X-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)
11.76260.4786-1.05523.07650.06690.3827-0.11481.303-1.1545-1.14590.01990.08450.5986-0.74740.95921.0183-0.0367-0.16521.2446-0.03780.7164-6.524846.2549-27.8408
20.92650.4587-0.0371.0137-2.8445-0.86080.34150.0889-0.10850.26170.44880.56710.3827-0.15340.06671.023-0.08470.02550.84580.11371.0533-7.487725.09715.9277
31.2542-1.63640.01461.32090.80230.78760.0375-0.54070.24760.90680.07550.6999-1.46920.27750.00071.048-0.1128-0.04041.02360.16340.9055-6.013319.874617.0452
41.45641.67390.29591.43790.35980.06660.30350.5386-0.0070.16590.71941.07860.1772-0.5794-0.00080.87890.12130.02930.96340.1690.9383-5.486435.3731-5.0966
51.45960.4335-0.92960.44820.35391.88860.04510.37010.86070.01170.28050.5850.23510.09640.00091.11550.0917-0.22991.115-0.09661.134-10.555943.2964-26.1581
61.7278-1.2531-0.22782.4923-3.2574.84-0.2372-0.5255-0.54490.88760.257-0.7915-0.0485-0.1601-0.83350.56190.0538-0.18110.7526-0.02060.79676.853838.69290.5165
70.1255-0.29290.13770.5555-0.12090.16570.05590.1862-0.85441.45791.3875-1.5420.6507-0.1457-0.00180.96320.1560.15271.2645-0.29191.55274.222157.5973-13.3411
81.2021-0.81190.3850.5817-0.14870.66320.25130.08432.0473-0.9468-2.0975-0.77840.46380.0741-0.03640.6442-0.00980.04191.0364-0.03830.74493.637346.2343-14.5212
92.99370.0337-0.6933-0.0672-0.34772.18520.6983-0.75340.77830.4315-0.09860.7540.392-1.026900.70460.2079-0.18950.7442-0.00350.9202-6.37248.1667-7.442
101.0363-0.8409-0.3512.05941.56711.20370.1859-0.05362.623-0.6224-0.0095-1.9547-1.41271.18190.34681.43540.44170.17960.75050.29770.4486-3.677456.6595-12.3194
112.90491.6658-1.07851.1271.07362.14120.1038-0.6696-0.2451-0.6391-0.6983-2.0708-0.85060.453-0.02630.9653-0.0523-0.37250.59060.05420.54213.791744.2681-1.3919
123.5552-0.6205-3.58181.9032-0.46174.87530.2894-0.02480.46950.31240.1558-0.024-0.44560.21621.56450.54430.0659-0.02670.7960.0150.73438.554333.0485-11.2202
131.43551.0708-1.05432.5545-1.2570.7642-0.6061-1.06480.4581-0.0059-0.2301-0.61530.26610.7259-0.00130.7995-0.09090.07610.84150.02170.8835.369817.9602-1.6866
141.76870.0066-0.25940.2107-0.54651.18930.72221.2485-1.46750.581-0.4654-0.39570.6222-1.3672-0.02771.1154-0.18980.07780.86370.24471.4775-4.838220.0423-1.3543
152.0575-0.6521-0.93740.48240.58590.6758-0.1975-0.2735-3.45360.3268-0.65510.35930.8436-1.1963-0.4251.7301-0.2136-0.03080.38520.29222.1721-4.5459.7606-3.1272
163.1156-1.0040.10660.5026-0.1585-0.2867-0.05550.3472-0.3327-0.531-0.1976-0.32710.97720.4914-0.00160.9656-0.11470.14080.6786-0.01280.93958.574216.113-8.4124
171.024-0.71991.41421.95470.56382.6513-0.0869-0.275-0.23970.45140.0333-0.5815-0.61490.1555-0.35110.93440.2132-0.25161.0128-0.21941.198718.241430.45973.3799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resseq 4:11)
2X-RAY DIFFRACTION2chain 'D' and (resseq 12:27)
3X-RAY DIFFRACTION3chain 'C' and (resseq 4:12)
4X-RAY DIFFRACTION4chain 'C' and (resseq 13:19)
5X-RAY DIFFRACTION5chain 'C' and (resseq 20:26)
6X-RAY DIFFRACTION6chain 'A' and (resseq 9:48)
7X-RAY DIFFRACTION7chain 'A' and (resseq 49:58)
8X-RAY DIFFRACTION8chain 'A' and (resseq 59:69)
9X-RAY DIFFRACTION9chain 'A' and (resseq 70:89)
10X-RAY DIFFRACTION10chain 'A' and (resseq 90:102)
11X-RAY DIFFRACTION11chain 'A' and (resseq 103:147)
12X-RAY DIFFRACTION12chain 'B' and (resseq 9:33)
13X-RAY DIFFRACTION13chain 'B' and (resseq 34:69)
14X-RAY DIFFRACTION14chain 'B' and (resseq 70:82)
15X-RAY DIFFRACTION15chain 'B' and (resseq 83:90)
16X-RAY DIFFRACTION16chain 'B' and (resseq 91:130)
17X-RAY DIFFRACTION17chain 'B' and (resseq 131:149)

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