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- PDB-3qf3: Crystal structure of EspR transcription factor from mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 3qf3
TitleCrystal structure of EspR transcription factor from mycobacterium tuberculosis
ComponentsESX-1 secretion-associated regulator EspR
KeywordsTRANSCRIPTION / N-terminal HTH motif / C-terminal dimerization domain / Transcription factor / homodimer
Function / homology
Function and homology information


response to host immune response / nucleoid / regulation of protein secretion / peptidoglycan-based cell wall / regulation of DNA-templated transcription / DNA binding / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / D-MALATE / Nucleoid-associated protein EspR / Nucleoid-associated protein EspR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsBlasco, B. / Pojer, F. / Cole, S.T.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis.
Authors: Blasco, B. / Stenta, M. / Alonso-Sarduy, L. / Dietler, G. / Peraro, M.D. / Cole, S.T. / Pojer, F.
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Jan 30, 2013Group: Non-polymer description
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESX-1 secretion-associated regulator EspR
D: ESX-1 secretion-associated regulator EspR
B: ESX-1 secretion-associated regulator EspR
C: ESX-1 secretion-associated regulator EspR
E: ESX-1 secretion-associated regulator EspR
F: ESX-1 secretion-associated regulator EspR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8529
Polymers88,4506
Non-polymers4023
Water4,179232
1
A: ESX-1 secretion-associated regulator EspR
D: ESX-1 secretion-associated regulator EspR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6173
Polymers29,4832
Non-polymers1341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-26 kcal/mol
Surface area13230 Å2
MethodPISA
2
B: ESX-1 secretion-associated regulator EspR
C: ESX-1 secretion-associated regulator EspR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6173
Polymers29,4832
Non-polymers1341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-27 kcal/mol
Surface area13020 Å2
MethodPISA
3
E: ESX-1 secretion-associated regulator EspR
F: ESX-1 secretion-associated regulator EspR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6173
Polymers29,4832
Non-polymers1341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-26 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.209, 81.702, 124.798
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains 6 monomers. The biological assembly is an homodimer containing chains C and D / The asymmetric unit contains 6 monomers. The biological assembly is an homodimer containing chains E and F / The asymmetric unit contains 6 monomers. The biological assembly is an homodimer containing chains D and A

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Components

#1: Protein
ESX-1 secretion-associated regulator EspR


Mass: 14741.597 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: espR, MT3964, Rv3849 / Plasmid: pHis9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P96228, UniProt: P9WJB7*PLUS
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3 Å3/Da / Density % sol: 58.95 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.2 M malic acid, pH 7, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→36.92 Å / Num. obs: 74014 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.18 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.28
Reflection shellResolution: 2.41→2.56 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.651 / % possible all: 96.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Using our 2.8A SAD solved structure of a seleno-methionine derivative crystal of EspR

Resolution: 2.41→36.92 Å / SU ML: 0.39 / σ(F): 2.01 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 2013 5 %
Rwork0.1839 --
obs0.1868 40265 99.56 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.165 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0876 Å2-0 Å20.8601 Å2
2---2.8084 Å2-0 Å2
3---2.7208 Å2
Refinement stepCycle: LAST / Resolution: 2.41→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6113 0 27 232 6372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086277
X-RAY DIFFRACTIONf_angle_d0.9998485
X-RAY DIFFRACTIONf_dihedral_angle_d14.4482370
X-RAY DIFFRACTIONf_chiral_restr0.062922
X-RAY DIFFRACTIONf_plane_restr0.0051126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4105-2.49660.33681950.24673705X-RAY DIFFRACTION97
2.4966-2.59650.30022000.24523801X-RAY DIFFRACTION100
2.5965-2.71470.32172010.23513812X-RAY DIFFRACTION100
2.7147-2.85770.29462010.22073811X-RAY DIFFRACTION100
2.8577-3.03670.28412020.22783844X-RAY DIFFRACTION100
3.0367-3.27110.27272020.20573839X-RAY DIFFRACTION100
3.2711-3.60.26332010.19663813X-RAY DIFFRACTION100
3.6-4.12030.23772010.17233825X-RAY DIFFRACTION100
4.1203-5.18890.17222040.13863879X-RAY DIFFRACTION100
5.1889-36.92410.21582060.15943923X-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)
12.07260.780.76372.36352.57083.5475-0.5918-0.5140.31850.01180.196-0.0679-0.5345-0.67940.33530.48980.3522-0.24120.4826-0.16650.32832.53612.87467.2558
21.1288-1.00061.08071.73561.02616.0828-0.29160.13-0.10180.19460.17470.27150.76290.77030.03520.37310.1121-0.0110.2670.03540.245920.093-10.450515.6813
32.3821-0.34721.95540.48190.18688.40090.6284-0.1572-0.09440.1594-0.0684-0.06512.1003-0.4659-0.49350.7319-0.1829-0.10120.17550.00280.174-1.0915-7.565-37.222
41.46240.29460.69772.879-1.58432.8141-0.14030.1624-0.1450.2942-0.3443-0.3258-0.41080.19940.49310.2628-0.1558-0.04030.27940.04910.400816.624815.6545-29.0378
50.611-0.25791.70930.92050.17385.1676-0.02750.40950.2153-0.0329-0.0664-0.1178-0.08210.73620.09530.044-0.02480.00870.33540.02180.19010.4316.7566-56.6045
62.30951.83751.36172.57460.70690.9848-0.3560.5805-0.12710.14560.04290.1608-0.29210.22170.23680.4045-0.1572-0.12050.40610.01930.484716.338718.2979-32.0319
72.13660.1890.79520.8073-0.39684.0338-0.3127-0.04250.0825-0.31130.176-0.11430.4556-0.37160.04850.3688-0.0845-0.03860.12840.02020.14072.26560.7901-13.5862
80.3046-0.29591.28731.4229-0.28594.71580.08440.12450.222-0.28140.07720.00740.93941.0235-0.13430.43420.1548-0.04560.3796-0.04810.320419.3014-9.48957.41
92.57650.07011.1043.76450.261.3884-0.0394-0.3725-0.04120.59490.00670.2726-0.2311-0.87970.060.26180.03750.10480.5982-0.08050.132613.9906-28.7573-41.8258
101.1468-0.60630.70991.1553-0.16753.382-0.09280.5518-0.0384-0.0231-0.0426-0.2442-0.07180.9880.14750.1101-0.12080.06570.5334-0.03980.306736.5787-30.7536-62.3252
111.62640.34341.93273.04580.63033.3640.0616-0.0153-0.09690.4146-0.3826-0.1297-0.47610.14140.20210.4104-0.2303-0.04760.31370.13020.21334.6004-29.2902-27.959
122.6518-0.99731.55530.4371-0.41171.3520.03570.4523-0.39540.1979-0.2281-0.0423-0.10750.61120.31260.0818-0.18420.08320.42760.01230.240238.7887-32.0791-58.4348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:95)
2X-RAY DIFFRACTION2(chain A and resid 96:133)
3X-RAY DIFFRACTION3(chain B and resid 3:93)
4X-RAY DIFFRACTION4(chain B and resid 94:133)
5X-RAY DIFFRACTION5(chain C and resid 3:91)
6X-RAY DIFFRACTION6(chain C and resid 92:131)
7X-RAY DIFFRACTION7(chain D and resid 4:80)
8X-RAY DIFFRACTION8(chain D and resid 81:131)
9X-RAY DIFFRACTION9(chain E and resid 3:94)
10X-RAY DIFFRACTION10(chain E and resid 95:133)
11X-RAY DIFFRACTION11(chain F and resid 3:89)
12X-RAY DIFFRACTION12(chain F and resid 90:132)

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