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- PDB-3poa: Structural and functional analysis of phosphothreonine-dependent ... -

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Basic information

Entry
Database: PDB / ID: 3poa
TitleStructural and functional analysis of phosphothreonine-dependent FHA domain interactions
Components
  • Putative uncharacterized protein TB39.8
  • synthetic phosphopeptide
KeywordsPEPTIDE BINDING PROTEIN / FHA domain / synthetic phosphopeptide
Function / homology
Function and homology information


peptidoglycan-based cell wall / mRNA binding / cytosol
Similarity search - Function
FhaA, N-terminal domain / FhaA, N-terminal domain superfamily / FhaA, N-terminal domain / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain ...FhaA, N-terminal domain / FhaA, N-terminal domain superfamily / FhaA, N-terminal domain / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
FHA domain-containing protein FhaA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsPennell, S. / Smerdon, S.J.
CitationJournal: Structure / Year: 2010
Title: Structural and functional analysis of phosphothreonine-dependent FHA domain interactions
Authors: Pennell, S. / Westcott, S. / Ortiz-Lombardia, M. / Patel, D. / Li, J. / Nott, T.J. / Mohammed, D. / Buxton, R.S. / Yaffe, M.B. / Verma, C. / Smerdon, S.J.
History
DepositionNov 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein TB39.8
B: synthetic phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4603
Polymers12,3952
Non-polymers651
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-4 kcal/mol
Surface area5790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.016, 74.425, 63.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-106-

HOH

21B-211-

HOH

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Components

#1: Protein Putative uncharacterized protein TB39.8 / Rv0020c protein


Mass: 10947.088 Da / Num. of mol.: 1 / Fragment: FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: Rv0020c / Production host: Escherichia coli (E. coli) / References: UniProt: P71590
#2: Protein/peptide synthetic phosphopeptide


Mass: 1447.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.2 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.01→19.05 Å / Num. obs: 8693

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→19.05 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.911 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23706 422 4.9 %RANDOM
Rwork0.17877 ---
obs0.18167 8693 93.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.611 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.56 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.01→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 1 234 1038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021814
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9591106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57923.90241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60515135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.068159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5961.5507
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1842817
X-RAY DIFFRACTIONr_scbond_it2.0753307
X-RAY DIFFRACTIONr_scangle_it3.6214.5289
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 19 -
Rwork0.185 429 -
obs--67.17 %
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)
11.32620.3612-0.38420.8492-0.43641.82190.0065-0.05850.0196-0.01830.03870.0389-0.020.0509-0.04520.05270.00150.00750.0298-0.02460.058214.937221.551231.1926
217.6795-5.1193-9.190312.52217.4089.6076-0.0002-0.197-0.278-0.2119-0.25560.15390.2228-0.38230.25590.0394-0.03610.00610.13240.02520.0226.632911.025243.7843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 99
2X-RAY DIFFRACTION2B2 - 8

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