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- PDB-4pac: Crystal Structure of Histidine-containing Phosphotransfer Protein... -

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Basic information

Entry
Database: PDB / ID: 4pac
TitleCrystal Structure of Histidine-containing Phosphotransfer Protein AHP2 from Arabidopsis thaliana
ComponentsHistidine-containing phosphotransfer protein 2
KeywordsSIGNALING PROTEIN / cytokinin signaling / helical fold
Function / homology
Function and homology information


antipodal cell differentiation / embryo sac egg cell differentiation / protein histidine kinase binding / cytokinin-activated signaling pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / phosphorylation / nucleus / cytosol / cytoplasm
Similarity search - Function
HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / Histidine-containing phosphotransfer protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.53 Å
AuthorsDegtjarik, O. / Dopitova, R. / Puehringer, S. / Weiss, M.S. / Janda, L. / Hejatko, J. / Kuta-Smatanova, I.
Funding support Czech Republic, 6items
OrganizationGrant numberCountry
Czech Science Foundation521/09/1699 Czech Republic
Czech Science FoundationP305/11/0756, Czech Republic
Central European Institute of TechnologyCZ.1.05/1.1.00/02.0068 Czech Republic
Czech Academy of SciencesAV0Z60870520 Czech Republic
ME09016 Czech Republic
CZ.1.05/2.1.00/01.0024 Czech Republic
CitationJournal: To Be Published
Title: Crystal structure of AHP2 from Arabidopsis thaliana
Authors: Degtjarik, O. / Dopitova, R. / Puehringer, S. / Reha, D. / Otrusinova, O. / Pekarova, B. / Kuty, M. / Zidek, L. / Janda, L. / Weiss, M.S. / Kuta-Smatanova, I. / Hejatko, H.
History
DepositionApr 8, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1May 8, 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: Histidine-containing phosphotransfer protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6343
Polymers22,3691
Non-polymers2642
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint8 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 59.900, 169.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Histidine-containing phosphotransfer protein 2


Mass: 22369.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHP2, ATHP1, At3g29350, MUO10.6 / Plasmid: pRSET B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q9ZNV8
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1M MES, 1.6M magnesium sulfate / PH range: 5.8 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 10808 / % possible obs: 99.6 % / Redundancy: 7 % / Net I/σ(I): 15.7
Reflection shellResolution: 2.53→2.68 Å / % possible obs: 98.7 % / Redundancy: 7.02 % / Rmerge(I) obs: 1.014 / Mean I/σ(I) obs: 1.76

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
MAR345dtbdata collection
SHELXDEphasing
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.53→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.856 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30392 443 4.8 %RANDOM
Rwork0.22869 ---
obs0.23219 8855 84.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.628 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--0.97 Å2-0 Å2
3----1.94 Å2
Refinement stepCycle: 1 / Resolution: 2.53→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 17 18 1243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191245
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9821669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1135151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42825.6958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.9715235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.79155
X-RAY DIFFRACTIONr_chiral_restr0.1210.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02898
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_it5.2735.737610
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.048.567759
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.5156.073635
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.87447.2581902
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.528→2.594 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.55 17 -
Rwork0.479 374 -
obs--49.94 %

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