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- PDB-4g78: Subatomic Resolution Crystal Structure of Histidine-containing Ph... -

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Basic information

Entry
Database: PDB / ID: 4g78
TitleSubatomic Resolution Crystal Structure of Histidine-containing Phosphotransfer Protein MtHPt2 from Medicago truncatula
ComponentsHistidine phosphotransfer protein
KeywordsTRANSFERASE / SUBATOMIC RESOLUTION / HELIX BUNDLE / PLANT HORMONE SIGNAL TRANSDUCTION / HISTIDINE KINASE
Function / homology
Function and homology information


protein histidine kinase binding / cytokinin-activated signaling pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / nucleus / cytoplasm / cytosol
Similarity search - Function
Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / 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
Histidine-containing phosphotransfer protein
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.92 Å
AuthorsRuszkowski, M. / Sikorski, M. / Jaskolski, M.
Citation
Journal: To be Published
Title: Subatomic Resolution Crystal Structure of Histidine-containing Phosphotransfer Protein MtHPt2 from Medicago truncatula
Authors: Ruszkowski, M. / Sikorski, M. / Jaskolski, M.
#1: Journal: Plant Cell / Year: 2006
Title: The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling.
Authors: Hutchison, C.E. / Li, J. / Argueso, C. / Gonzalez, M. / Lee, E. / Lewis, M.W. / Maxwell, B.B. / Perdue, T.D. / Schaller, G.E. / Alonso, J.M. / Ecker, J.R. / Kieber, J.J.
#2: Journal: Protein Sci. / Year: 2005
Title: Crystal structure of the histidine-containing phosphotransfer protein ZmHP2 from maize.
Authors: Sugawara, H. / Kawano, Y. / Hatakeyama, T. / Yamaya, T. / Kamiya, N. / Sakakibara, H.
#3: Journal: J.Mol.Biol. / Year: 1999
Title: Conservation of structure and function among histidine-containing phosphotransfer (HPt) domains as revealed by the crystal structure of YPD1.
Authors: Xu, Q. / West, A.H.
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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

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Assembly

Deposited unit
A: Histidine phosphotransfer protein


Theoretical massNumber of molelcules
Total (without water)17,4761
Polymers17,4761
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.240, 50.150, 50.380
Angle α, β, γ (deg.)90.00, 97.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histidine phosphotransfer protein


Mass: 17475.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MtHPt2, MTR_1g089130, MTR_1g089350 / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: G7I2T8, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 32.01 %
Crystal growTemperature: 292 K / pH: 6.5
Details: 0.09M Halogens, 0.1M buffer system 1, 30% PEG 550MME + PEG 20K (Molecular Dimensions Morpheus Screen B1), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2012 / Details: FOCUSING MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 0.92→50 Å / Num. obs: 84634 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 13.232 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 21.78
Reflection shellResolution: 0.92→0.94 Å / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.89 / % possible all: 75.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å25.11 Å
Translation2.5 Å25.11 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
SHELXrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3US6

3us6


Resolution: 0.92→50 Å / Cross valid method: R-FREE / Stereochemistry target values: Engh & Huber / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.155 1008 -RAMDOM
Rwork0.121 ---
obs0.121 79313 97.8 %-
all-84634 --
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 19.627 Å2
Refinement stepCycle: LAST / Resolution: 0.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 0 207 1389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.023
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.3
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.157
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 0.92→0.96 Å / Rfactor Rwork: 0.271

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