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- PDB-2ff4: Mycobacterium tuberculosis EmbR in complex with low affinity phos... -

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Basic information

Entry
Database: PDB / ID: 2ff4
TitleMycobacterium tuberculosis EmbR in complex with low affinity phosphopeptide
Components
  • DNA repair protein RAD9
  • Probable regulatory protein embR
KeywordsTRANSCRIPTION / winged-helix / tetratricopeptide repeat / beta-sandwich
Function / homology
Function and homology information


negative regulation of DNA strand resection involved in replication fork processing / SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cell wall / mitotic intra-S DNA damage checkpoint signaling / phosphorelay signal transduction system / enzyme activator activity / mitotic G1 DNA damage checkpoint signaling / peptidoglycan-based cell wall / DNA damage checkpoint signaling ...negative regulation of DNA strand resection involved in replication fork processing / SUMOylation of transcription factors / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cell wall / mitotic intra-S DNA damage checkpoint signaling / phosphorelay signal transduction system / enzyme activator activity / mitotic G1 DNA damage checkpoint signaling / peptidoglycan-based cell wall / DNA damage checkpoint signaling / nucleotide-excision repair / double-strand break repair / histone binding / double-stranded DNA binding / regulation of cell cycle / DNA repair / GTPase activity / regulation of DNA-templated transcription / chromatin / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / plasma membrane
Similarity search - Function
Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Rad9-like Rad53-binding domain, fungi / Fungal Rad9-like Rad53-binding / : / : / Tumour Suppressor Smad4 - #20 / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain ...Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Bacterial transcriptional activator domain / Rad9-like Rad53-binding domain, fungi / Fungal Rad9-like Rad53-binding / : / : / Tumour Suppressor Smad4 - #20 / OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT 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
DNA repair protein RAD9 / Transcriptional regulatory protein EmbR / Transcriptional regulatory protein EmbR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 19, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable regulatory protein embR
B: Probable regulatory protein embR
E: DNA repair protein RAD9
F: DNA repair protein RAD9


Theoretical massNumber of molelcules
Total (without water)86,0654
Polymers86,0654
Non-polymers00
Water9,584532
1
A: Probable regulatory protein embR
E: DNA repair protein RAD9


Theoretical massNumber of molelcules
Total (without water)43,0322
Polymers43,0322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-3 kcal/mol
Surface area18670 Å2
MethodPISA
2
B: Probable regulatory protein embR
F: DNA repair protein RAD9


Theoretical massNumber of molelcules
Total (without water)43,0322
Polymers43,0322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-3 kcal/mol
Surface area18150 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-14 kcal/mol
Surface area33680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.390, 82.040, 81.080
Angle α, β, γ (deg.)90.00, 115.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable regulatory protein embR


Mass: 41988.375 Da / Num. of mol.: 2
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: Protein/peptide DNA repair protein RAD9


Mass: 1043.963 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The sequence of the peptide is naturally found in Saccharomyces cerevisiae (yeast).
References: UniProt: P14737
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 2.5% PEG 8000, 3% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→46.6 Å / Num. all: 75792 / Num. obs: 75792 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 5 / Num. unique all: 11024 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.021 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23941 3773 5 %RANDOM
Rwork0.21523 ---
all0.21644 72016 --
obs0.21644 72016 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20.26 Å2
2---0.81 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 0 532 6377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215959
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.9588115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2015762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5722.799268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31815936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8171561
X-RAY DIFFRACTIONr_chiral_restr0.0760.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024561
X-RAY DIFFRACTIONr_nbd_refined0.1880.22616
X-RAY DIFFRACTIONr_nbtor_refined0.2920.24013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2439
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.223
X-RAY DIFFRACTIONr_mcbond_it0.4541.53938
X-RAY DIFFRACTIONr_mcangle_it0.72326102
X-RAY DIFFRACTIONr_scbond_it1.17632282
X-RAY DIFFRACTIONr_scangle_it1.9154.52013
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 252 -
Rwork0.34 5316 -
obs--100 %
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)
10.39590.0484-0.00351.43370.05460.32030.0367-0.060100.0324-0.05560.03-0.0701-0.04470.0189-0.07940.0025-0.0004-0.06960.0123-0.1093-26.48768.51860.6873
20.5821-0.14910.00771.5688-0.22930.4753-0.00840.1038-0.0938-0.0957-0.05050.02250.02520.01050.0589-0.088-0.01660.0148-0.056-0.0121-0.1015-13.3213-6.4996-24.5539
329.009-5.4577-0.06546.2922-2.518639.8708-0.23980.459-1.1485-0.51620.53340.49971.76690.0819-0.29360.00040.00020.00070.0006-0.00060.0009-43.4957-1.2896-21.0982
470.03295.9048-14.806438.26918.451623.8617-0.278-0.49310.206-0.65790.1669-0.06530.2758-0.81380.11120.00070.00090.00080.0009-0.00020.0015-43.4992-0.4511-27.323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 3868 - 386
2X-RAY DIFFRACTION2BB8 - 3808 - 380
3X-RAY DIFFRACTION3EC1 - 71 - 7
4X-RAY DIFFRACTION4FD3 - 73 - 7

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