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- PDB-2fez: Mycobacterium tuberculosis EmbR -

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Basic information

Entry
Database: PDB / ID: 2fez
TitleMycobacterium tuberculosis EmbR
ComponentsProbable regulatory protein embR
KeywordsTRANSCRIPTION / transcriptional regulator / winged-helix / tetratricopeptide repeat / beta-sandwich
Function / homology
Function and homology information


cell wall / phosphorelay signal transduction system / peptidoglycan-based cell wall / GTPase activity / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / plasma membrane
Similarity search - Function
Bacterial transcriptional activator domain / : / Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Tumour Suppressor Smad4 - #20 / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Tumour Suppressor Smad4 ...Bacterial transcriptional activator domain / : / Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Tumour Suppressor Smad4 - #20 / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Tumour Suppressor Smad4 / Signal transduction response regulator, C-terminal effector / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Tetratricopeptide repeat domain / SMAD/FHA domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulatory protein EmbR / Transcriptional regulatory protein EmbR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsFutterer, K. / Alderwick, L.J. / Besra, G.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Molecular structure of EmbR, a response element of Ser/Thr kinase signaling in Mycobacterium tuberculosis
Authors: Alderwick, L.J. / Molle, V. / Kremer, L. / Cozzone, A.J. / Dafforn, T.R. / Besra, G.S. / Futterer, K.
History
DepositionDec 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable regulatory protein embR


Theoretical massNumber of molelcules
Total (without water)41,9881
Polymers41,9881
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.172, 83.614, 140.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Probable regulatory protein embR


Mass: 41988.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: embR / Plasmid: pET23c / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P66799, UniProt: P9WGJ9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Na-Hepes, pH 7.5, 15% PEG 4000, 0.2 M magnesium choride, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-310.931
SYNCHROTRONESRF BM1420.9783,0.9887,0.9686
Detector
TypeIDDetectorDate
MARRESEARCH1CCDNov 28, 2004
MARRESEARCH2CCDNov 28, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9311
20.97831
30.98871
40.96861
ReflectionResolution: 2→44.4 Å / Num. all: 31575 / Num. obs: 31575 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 10 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4565 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→42 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.441 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.149
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.22842 1591 5 %RANDOM
Rwork0.20727 ---
all0.20837 29959 --
obs0.20837 29959 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.521 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---0.93 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 0 240 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212904
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9553956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0235372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78922.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7815456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3181531
X-RAY DIFFRACTIONr_chiral_restr0.0730.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022228
X-RAY DIFFRACTIONr_nbd_refined0.1870.21323
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21974
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2203
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4020.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.213
X-RAY DIFFRACTIONr_mcbond_it0.4431.51909
X-RAY DIFFRACTIONr_mcangle_it0.76722978
X-RAY DIFFRACTIONr_scbond_it1.24931112
X-RAY DIFFRACTIONr_scangle_it2.0734.5978
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 118 -
Rwork0.259 2184 -
obs--99.91 %
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)
11.8931-0.26080.45023.6728-0.97792.3380.0140.04910.08610.1785-0.0466-0.0677-0.10650.16620.0326-0.111-0.030.0337-0.11480.0094-0.119717.79554.64749.643
21.63610.72290.37393.0626-0.47750.9890.1994-0.0545-0.30410.2782-0.1346-0.12660.04610.0807-0.0649-0.0478-0.0125-0.0232-0.0607-0.0059-0.042511.37322.74856.58
32.5223-0.65740.16254.43950.9885.66620.00310.13940.0306-0.171-0.13410.1089-0.1242-0.02420.131-0.12230.00860.0235-0.1044-0.0258-0.083914.12833.47633.353
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 10510 - 105
2X-RAY DIFFRACTION2AA107 - 285107 - 285
3X-RAY DIFFRACTION3AA286 - 382286 - 382

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