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- PDB-3zvu: Structure of the PYR1 His60Pro mutant in complex with the HAB1 ph... -

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Basic information

Entry
Database: PDB / ID: 3zvu
TitleStructure of the PYR1 His60Pro mutant in complex with the HAB1 phosphatase and Abscisic acid
Components
  • ABSCISIC ACID RECEPTOR PYR1
  • PROTEIN PHOSPHATASE 2C 16
KeywordsRECEPTOR/HYDROLASE / RECEPTOR-HYDROLASE COMPLEX / HORMONE RECEPTOR / STRESS RESPONSE
Function / homology
Function and homology information


positive regulation of response to water deprivation / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / ubiquitin-like protein ligase binding / signaling receptor activity ...positive regulation of response to water deprivation / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Polyketide cyclase / dehydrase and lipid transport / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain ...Polyketide cyclase / dehydrase and lipid transport / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A8S / : / Abscisic acid receptor PYR1 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBetz, K. / Dupeux, F. / Santiago, J. / Rodriguez, P.L. / Marquez, J.A.
CitationJournal: Embo J. / Year: 2011
Title: A Thermodynamic Switch Modulates Abscisic Acid Receptor Sensitivity.
Authors: Dupeux, F. / Santiago, J. / Betz, K. / Twycross, J. / Park, S. / Rodriguez, L. / Gonzalez-Guzman, M. / Jensen, M.R. / Krasnogor, N. / Blackledge, M. / Holdsworth, M. / Cutler, S.R. / ...Authors: Dupeux, F. / Santiago, J. / Betz, K. / Twycross, J. / Park, S. / Rodriguez, L. / Gonzalez-Guzman, M. / Jensen, M.R. / Krasnogor, N. / Blackledge, M. / Holdsworth, M. / Cutler, S.R. / Rodriguez, P.L. / Marquez, J.A.
History
DepositionJul 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_asym_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_asym_id / _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_asym_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: ABSCISIC ACID RECEPTOR PYR1
B: PROTEIN PHOSPHATASE 2C 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5787
Polymers59,0122
Non-polymers5665
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-55.1 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.480, 66.050, 172.390
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 ABSCISIC ACID RECEPTOR PYR1 / ABI1-BINDING PROTEIN 6 / PROTEIN PYRABACTIN RESISTANCE 1 / REGULATORY COMPONENTS OF ABA RECEPTOR 11


Mass: 21664.307 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-191 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O49686
#2: Protein PROTEIN PHOSPHATASE 2C 16 / ATPP2C16 / ATP2C-HA / PROTEIN HYPERSENSITIVE TO ABA 1 / PROTEIN PHOSPHATASE 2C HAB1 / PP2C HAB1


Mass: 37347.824 Da / Num. of mol.: 1
Fragment: HAB1 PHOSPHATASE CATALYTIC REGION, RESIDUES 178-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase

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Non-polymers , 4 types, 211 molecules

#3: Chemical ChemComp-A8S / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / (+)-abscisic acid / (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid


Mass: 264.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAIN A VARIANT WAS GENERATED FROM SWISS-PROT ENTRY O49686.1. CHAIN B SEQUENCE WAS GENERATED FROM ...CHAIN A VARIANT WAS GENERATED FROM SWISS-PROT ENTRY O49686.1. CHAIN B SEQUENCE WAS GENERATED FROM GENBANK ENTRY AEE35372.1.

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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: 2.21 Å3/Da / Density % sol: 44.39 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7.5 / Details: 0.25M AMSO4, 19% PEG 3350 AT 20 DEG. C, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97924
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2011 / Details: SILICON TOROIDAL MIRROR COATED WITH RHODIUM
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.1→24.29 Å / Num. obs: 31132 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.14 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.7
Reflection shellResolution: 2.2→2.21 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.42 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0107refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QN1

3qn1


Resolution: 2.1→24.29 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.88 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23567 1557 5 %RANDOM
Rwork0.18008 ---
obs0.18282 29575 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.807 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2---0.37 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 31 206 3935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223802
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9585147
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03623.647170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16715651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2581530
X-RAY DIFFRACTIONr_chiral_restr0.1270.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212844
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 102 -
Rwork0.23 1969 -
obs--99.86 %

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