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- PDB-5or6: Crystal structures of PYR1/HAB1 in complex with synthetic analogu... -

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Basic information

Entry
Database: PDB / ID: 5or6
TitleCrystal structures of PYR1/HAB1 in complex with synthetic analogues of Abscisic Acid
Components
  • Abscisic acid receptor PYR1
  • Protein phosphatase 2C 16
KeywordsPROTEIN BINDING / Complex Arabidopsis hab1-pyr1
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 activity / myosin phosphatase activity / protein-serine/threonine phosphatase ...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 activity / myosin phosphatase activity / protein-serine/threonine phosphatase / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
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-A4K / : / Abscisic acid receptor PYR1 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFreigang, J.
CitationJournal: Eur.J.Org.Chem. / Year: 2018
Title: Insights into the in Vitro and in Vivo SAR of Abscisic Acid - Exploring Unprecedented Variations of the Side Chain via Cross-Coupling-Mediated Syntheses
Authors: Frackenpohl, J. / Grill, E. / Bojack, G. / Baltz, R. / Busch, M. / Dittgen, J. / Franke, J. / Freigang, J. / Gonzalez, S. / Heinemann, I. / Helmke, H. / Hills, M. / Hohmann, S. / von Koskull- ...Authors: Frackenpohl, J. / Grill, E. / Bojack, G. / Baltz, R. / Busch, M. / Dittgen, J. / Franke, J. / Freigang, J. / Gonzalez, S. / Heinemann, I. / Helmke, H. / Hills, M. / Hohmann, S. / von Koskull-Doering, P. / Kleemann, J. / Lange, G. / Lehr, S. / Mueller, T. / Peschel, E. / Poree, F. / Schmutzler, D. / Schulz, A. / Willms, L. / Wunschel, C.
History
DepositionAug 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)59,5346
Polymers59,0532
Non-polymers4814
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-30 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.182, 65.663, 171.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Abscisic acid receptor PYR1 / ABI1-binding protein 6 / Protein PYRABACTIN RESISTANCE 1 / Regulatory components of ABA receptor 11


Mass: 21705.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYR1, ABIP6, RCAR11, At4g17870, T6K21.50 / Production host: Escherichia coli (E. coli) / 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase
#3: Chemical ChemComp-A4K / (~{E})-3-(trifluoromethyl)-5-[(1~{S})-2,6,6-trimethyl-1-oxidanyl-4-oxidanylidene-cyclohex-2-en-1-yl]pent-2-en-4-ynoic acid


Mass: 316.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15F3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 20% Peg 8000, 100 mM Tris pH 8.5, 160 mM MgCl2, 60 mM glycylglycylglycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Apr 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 20069 / % possible obs: 97 % / Redundancy: 3.4 % / Rsym value: 0.1 / Net I/σ(I): 10.53
Reflection shellResolution: 2.4→2.55 Å / Rsym value: 0.351

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QN1

3qn1


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.843 / SU B: 11.599 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.739 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29025 1023 5.1 %RANDOM
Rwork0.21858 ---
obs0.22227 18884 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--1.09 Å20 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 25 465 4164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223763
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.911.9595094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3165468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.05523.571168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33215642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0011530
X-RAY DIFFRACTIONr_chiral_restr0.0610.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212823
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_it0.3741.52351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68923784
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6131412
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0744.51310
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 69 -
Rwork0.304 1224 -
obs--89.17 %

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