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- PDB-3qwg: Crystal structure of EspRdelta10, C-terminal 10 amino acids delet... -

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Basic information

Entry
Database: PDB / ID: 3qwg
TitleCrystal structure of EspRdelta10, C-terminal 10 amino acids deletion mutant of EspR transcription factor from Mycobacterium tuberculosis
ComponentsESX-1 secretion-associated regulator EspR
KeywordsTRANSCRIPTION / N-terminal helix-turn-helix motif / Transcription factor
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
Nucleoid-associated protein EspR / Nucleoid-associated protein EspR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.992 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
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
B: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)27,2572
Polymers27,2572
Non-polymers00
Water2,378132
1
A: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)13,6281
Polymers13,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)13,6281
Polymers13,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ESX-1 secretion-associated regulator EspR

B: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)27,2572
Polymers27,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area2000 Å2
ΔGint-8 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.460, 55.370, 76.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13628.368 Da / Num. of mol.: 2 / Fragment: unp residues 2-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: espR, MT3964, Rv3849 / Plasmid: pHis9gw / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96228, UniProt: P9WJB7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.81 Å3/Da / Density % sol: 31.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 4000, 100mM Tris-HCl, 200 mM LiSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0097 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0097 Å / Relative weight: 1
ReflectionResolution: 1.99→44.86 Å / Num. obs: 24707 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.83
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 3.02 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.11 / Num. unique all: 3522 / % possible all: 82.6

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4model building
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
CCP4phasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QF3

3qf3


Resolution: 1.992→44.86 Å / SU ML: 0.26 / σ(F): 2 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 680 4.96 %
Rwork0.1826 --
obs0.1852 13705 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.627 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.031 Å20 Å20 Å2
2--0.2098 Å2-0 Å2
3----0.2408 Å2
Refinement stepCycle: LAST / Resolution: 1.992→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 0 132 1570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071476
X-RAY DIFFRACTIONf_angle_d0.9452003
X-RAY DIFFRACTIONf_dihedral_angle_d13.933539
X-RAY DIFFRACTIONf_chiral_restr0.055219
X-RAY DIFFRACTIONf_plane_restr0.004259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9916-2.14530.25731250.19912393X-RAY DIFFRACTION91
2.1453-2.36120.27351510.18932577X-RAY DIFFRACTION99
2.3612-2.70290.26271430.18572619X-RAY DIFFRACTION99
2.7029-3.40520.21831210.17952652X-RAY DIFFRACTION99
3.4052-44.87530.22141400.17892784X-RAY DIFFRACTION99
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)
11.1535-0.21541.07180.39880.14391.1583-0.0603-0.21230.16390.12440.0192-0.12840.0942-0.13210.00180.21490.0028-0.02850.1820.00340.17753.736-10.5293-11.0922
20.64380.37680.32622.36960.34261.0542-0.01990.03690.1243-0.3116-0.1410.46970.03430.1541-0.02190.16660.00440.05090.12630.02490.19679.0605-5.9417-22.5696
30.23030.18390.13930.42420.17850.10740.06740.30640.06440.1087-0.0091-0.7606-0.22720.6698-0.16650.1598-0.0681-0.0250.31670.00810.380318.0276-11.1963-13.2603
40.1561-0.2273-0.31671.07750.44910.6967-0.0378-0.36060.3828-0.0652-0.0129-0.4137-0.28710.07510.01960.1495-0.0117-0.03250.2436-0.03450.22767.9027-1.0899-8.2053
50.0467-0.0656-0.0080.3329-0.23220.2725-0.0521-0.5257-0.27750.0099-0.1279-0.2432-0.00070.0340.06470.32710.00460.12970.34710.03060.3117-3.4686-5.772-2.9705
61.61560.388-0.40890.2149-0.50891.7307-0.07540.139-0.13620.21030.21090.16240.043-0.1961-0.05910.433-0.16580.09730.7306-0.10520.2764-9.3789-7.8919-11.1032
70.6904-0.26170.51490.60.21550.5584-0.21190.20580.4739-0.00260.0754-0.2311-0.14580.20570.0350.13230.0079-0.02660.1958-0.00330.185510.1408-22.112-17.4025
81.28360.472-0.17050.9265-0.14850.96880.40970.02-0.012-0.0584-0.42680.4302-0.331-0.3775-0.00650.25970.02630.03550.1615-0.0140.1701-1.1927-22.7045-13.6726
90.6070.08610.28820.32290.22340.2287-0.149-0.4867-0.00730.5053-0.21260.0304-0.25320.1467-0.09770.587-0.10590.0640.21550.113-0.12641.6295-28.5206-3.8235
100.1326-0.10550.01430.3664-0.09180.0331-0.0156-0.35530.11030.31440.1317-0.22720.11640.1553-0.04030.26390.0636-0.09350.2511-0.02710.21412.4741-20.9098-4.1412
110.643-0.0930.72911.18960.04710.75860.05110.2605-0.19580.28110.0318-0.40320.43650.59550.00350.24030.0819-0.05890.3031-0.02440.263212.8925-31.1881-15.2355
120.78511.5147-0.27063.0716-0.27990.6727-0.12020.15570.3927-0.21420.03310.26360.0664-0.1416-0.04060.2778-0.02150.11260.5199-0.04590.408412.1726-25.8397-28.1142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:22)
2X-RAY DIFFRACTION2(chain A and resid 23:41)
3X-RAY DIFFRACTION3(chain A and resid 42:56)
4X-RAY DIFFRACTION4(chain A and resid 57:82)
5X-RAY DIFFRACTION5(chain A and resid 83:91)
6X-RAY DIFFRACTION6(chain A and resid 92:96)
7X-RAY DIFFRACTION7(chain B and resid 4:20)
8X-RAY DIFFRACTION8(chain B and resid 21:34)
9X-RAY DIFFRACTION9(chain B and resid 35:45)
10X-RAY DIFFRACTION10(chain B and resid 46:56)
11X-RAY DIFFRACTION11(chain B and resid 57:83)
12X-RAY DIFFRACTION12(chain B and resid 84:93)

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