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- PDB-3us6: Crystal Structure of Histidine-containing Phosphotransfer Protein... -

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Basic information

Entry
Database: PDB / ID: 3us6
TitleCrystal Structure of Histidine-containing Phosphotransfer Protein MtHPt1 from Medicago truncatula
ComponentsHistidine-containing Phosphotransfer Protein type 1, MtHPt1
KeywordsTRANSFERASE / helix bundle / PLANT HORMONE SIGNAL TRANSDUCTION / CYTOKININ SIGNAL TRANSDUCTION / PHOSPHORYLATION / PHOSPHATE TRANSFER RELAY / RESPONSE REGULATOR / SIGNALING PROTEIN / CYTOKININ RECEPTOR CRE1
Function / homology
Function and homology information


multidimensional cell growth / embryo sac development / cytokinin-activated signaling pathway / protein histidine kinase binding / 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: 1.446 Å
AuthorsRuszkowski, M. / Brzezinski, K. / Jedrzejczak, R. / Dauter, M. / Dauter, Z. / Sikorski, M. / Jaskolski, M.
Citation
Journal: Febs J. / Year: 2013
Title: Medicago truncatula histidine-containing phosphotransfer protein: Structural and biochemical insights into the cytokinin transduction pathway in plants.
Authors: Ruszkowski, M. / Brzezinski, K. / Jedrzejczak, R. / Dauter, M. / Dauter, Z. / 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
DepositionNov 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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
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 type 1, MtHPt1


Theoretical massNumber of molelcules
Total (without water)17,7821
Polymers17,7821
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.554, 44.899, 85.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histidine-containing Phosphotransfer Protein type 1, MtHPt1


Mass: 17782.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MtHPt / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: B7FGU6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M BIS-TRIS, 25% PEG 3350, 0.2M AMMONIUM ACETATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2011 / Details: FOCUSING MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.446→50 Å / Num. all: 25816 / Num. obs: 25816 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 3.81 % / Biso Wilson estimate: 22.723 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.05
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.446-1.530.4262.023193173.7
1.53-1.640.2923.793855194.4
1.64-1.770.1976.463817199.8
1.77-1.940.1269.993538199.8
1.94-2.170.07117.293199199.7
2.17-2.50.05322.992836199.3
2.5-3.060.04327.842402198.8
3.06-4.320.03831.511903198.2
4.32-500.02931.91073194

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å31.04 Å
Translation2.5 Å31.04 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1yvi

1yvi


Resolution: 1.446→31.037 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.33 / Cross valid method: Rfree / Phase error: 17.8 / Stereochemistry target values: Engh & Huber / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 1002 3.88 %random
Rwork0.1675 ---
all0.1684 25816 --
obs0.1684 25813 94.34 %-
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.291 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso max: 151.57 Å2 / Biso mean: 23.0623 Å2 / Biso min: 7.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.9706 Å20 Å2-0 Å2
2--2.3054 Å2-0 Å2
3----3.276 Å2
Refinement stepCycle: LAST / Resolution: 1.446→31.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 0 159 1362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191281
X-RAY DIFFRACTIONf_angle_d1.6181736
X-RAY DIFFRACTIONf_chiral_restr0.106187
X-RAY DIFFRACTIONf_plane_restr0.01233
X-RAY DIFFRACTIONf_dihedral_angle_d14.49501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.446-1.52260.30781080.25442675278373
1.5226-1.6180.23591360.2073369350591
1.618-1.74290.19591500.171737283878100
1.7429-1.91830.20851500.174837003850100
1.9183-2.19580.19171500.153437353885100
2.1958-2.76620.18911520.1543761391399
2.7662-31.04450.16891560.16453843399997
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)
10.24280.04170.34320.0211-0.0070.7976-0.06730.16140.3063-0.2771-0.30840.0565-0.2045-0.1197-0.05860.20530.0192-0.01250.1044-0.01430.2054-7.282826.95025.9975
20.3231-0.35940.18830.6189-0.34330.47910.02710.13180.3395-0.1847-0.092-0.1372-0.15870.2235-0.04660.1161-0.017-0.00360.13090.00370.14725.975817.86610.7574
30.7495-0.1673-0.18380.38050.38950.5596-0.11570.0992-0.083-0.0725-0.0649-0.0648-0.0209-0.2663-0.12060.16050.01870.01060.190.0020.11294.46428.5349-0.0734
40.699-0.02260.17940.01390.01780.18550.1105-0.0251-0.0702-0.62650.0130.20090.271-0.0585-0.01950.25130.0307-0.01750.11450.0010.17716.1046-11.526718.8749
50.08460.08450.09570.08430.09840.2009-0.1351-0.0534-0.0623-0.38560.0286-0.32570.207-0.0523-0.10140.1910.03460.05990.15130.03170.167414.1431-4.341914.3564
60.0475-0.0328-0.10390.2037-0.0910.3724-0.0149-0.0283-0.04550.0141-0.1158-0.1990.02110.28780.01520.10650.0093-0.01210.15380.03190.143913.0356-1.266123.1612
70.30260.1430.07110.5150.30080.3164-0.03750.05840-0.08960.01280.00810.02580.0443-0.10650.0948-0.0172-0.00480.10070.01210.0922-1.569513.07448.6118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:8)A2 - 8
2X-RAY DIFFRACTION2(CHAIN A AND RESID 9:30)A9 - 30
3X-RAY DIFFRACTION3(CHAIN A AND RESID 31:53)A31 - 53
4X-RAY DIFFRACTION4(CHAIN A AND RESID 54:67)A54 - 67
5X-RAY DIFFRACTION5(CHAIN A AND RESID 68:87)A68 - 87
6X-RAY DIFFRACTION6(CHAIN A AND RESID 88:116)A88 - 116
7X-RAY DIFFRACTION7(CHAIN A AND RESID 117:148)A117 - 148

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