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- PDB-2r25: Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3- -

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Basic information

Entry
Database: PDB / ID: 2r25
TitleComplex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3-
Components
  • Osmosensing histidine protein kinase SLN1
  • Phosphorelay intermediate protein YPD1
KeywordsSignaling PROTEIN/Transferase / alpha5-beta5 / response regulator / four helix bundle / histidine phosphotransfer (HPt) protein / histidine kinase (HK) / Cytoplasm / Nucleus / Phosphorylation / Two-component regulatory system / Glycoprotein / Magnesium / Membrane / Metal-binding / Transferase / Transmembrane / Signaling PROTEIN-Transferase COMPLEX
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / protein histidine kinase binding / osmosensor activity / osmosensory signaling via phosphorelay pathway / histidine phosphotransfer kinase activity / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / cell periphery ...transferase activity, transferring phosphorus-containing groups / protein histidine kinase binding / osmosensor activity / osmosensory signaling via phosphorelay pathway / histidine phosphotransfer kinase activity / protein histidine kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / cell periphery / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain ...Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1 / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Osmosensing histidine protein kinase SLN1 / Phosphorelay intermediate protein YPD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsCopeland, D.M. / Zhao, X. / Soares, A.S. / West, A.H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog
Authors: Zhao, X. / Copeland, D.M. / Soares, A.S. / West, A.H.
History
DepositionAug 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphorelay intermediate protein YPD1
B: Osmosensing histidine protein kinase SLN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2515
Polymers34,1382
Non-polymers1133
Water4,288238
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.013, 75.544, 98.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Phosphorelay intermediate protein YPD1 / Histidine-containing phosphotransfer protein YPD1 / Tyrosine phosphatase-dependent protein 1


Mass: 19187.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07688
#2: Protein Osmosensing histidine protein kinase SLN1 / Osmolarity two-component system protein SLN1 / Tyrosine phosphatase-dependent protein 2


Mass: 14950.339 Da / Num. of mol.: 1 / Fragment: UNP residues 1086-1218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLN1, YPD2 / Production host: Escherichia coli (E. coli) / References: UniProt: P39928, histidine kinase

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Non-polymers , 4 types, 241 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 56.56 %
Crystal growTemperature: 295 K / pH: 5.6
Details: 2.2 M ammonium sulfate, 50 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 51329 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 28.8
Reflection shellResolution: 1.6→1.72 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.39 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.42 Å
Translation2.5 Å29.42 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QSP

1qsp


Resolution: 1.7→17.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.761 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2168 5 %RANDOM
Rwork0.196 ---
obs0.199 42989 99.2 %-
all-43353 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→17.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 6 238 2723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222505
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5651.9743385
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9055318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15326.218119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98615498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8351511
X-RAY DIFFRACTIONr_chiral_restr0.2520.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021857
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.21324
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21710
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.4450.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.79331546
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.99542514
X-RAY DIFFRACTIONr_scbond_it4.5644974
X-RAY DIFFRACTIONr_scangle_it6.3066868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 164 -
Rwork0.311 2928 -
obs--99.17 %

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