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- PDB-3rt0: Crystal structure of PYL10-HAB1 complex in the absence of abscisi... -

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Basic information

Entry
Database: PDB / ID: 3rt0
TitleCrystal structure of PYL10-HAB1 complex in the absence of abscisic acid (ABA)
Components
  • Abscisic acid receptor PYL10
  • Protein phosphatase 2C 16
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PYL10-HAB1 binary COMPLEX / apo-PYL10 inhibits HAB1 dephosphorylation activity / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


: / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / protein homodimerization activity / nucleus ...: / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / signaling receptor activity / protein homodimerization activity / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
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, 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
Abscisic acid receptor PYL10 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 Å
AuthorsHao, Q. / Yin, P. / Li, W. / Wang, L. / Yan, C. / Wang, J. / Yan, N.
CitationJournal: Mol.Cell / Year: 2011
Title: The Molecular Basis of ABA-Independent Inhibition of PP2Cs by a Subclass of PYL Proteins
Authors: Hao, Q. / Yin, P. / Li, W. / Wang, L. / Yan, C. / Lin, Z. / Wu, J.Z. / Wang, J. / Yan, S.F. / Yan, N.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ref_seq_dif.details / _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: Protein phosphatase 2C 16
B: Protein phosphatase 2C 16
C: Abscisic acid receptor PYL10
D: Abscisic acid receptor PYL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8726
Polymers116,8244
Non-polymers492
Water9,134507
1
A: Protein phosphatase 2C 16
C: Abscisic acid receptor PYL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4363
Polymers58,4122
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-10 kcal/mol
Surface area23790 Å2
MethodPISA
2
B: Protein phosphatase 2C 16
D: Abscisic acid receptor PYL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4363
Polymers58,4122
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-11 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.766, 83.503, 88.544
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 37753.219 Da / Num. of mol.: 2 / Fragment: residues 172- 511 / Mutation: C274S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase
#2: Protein Abscisic acid receptor PYL10 / ABI1-binding protein 8 / PYR1-like protein 10 / Regulatory components of ABA receptor 4


Mass: 20658.545 Da / Num. of mol.: 2 / Mutation: C166S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8H1R0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris, 21% PEG3350, 2% Dioxane , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 27, 2010
RadiationMonochromator: rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. obs: 58037 / % possible obs: 99.8 % / Biso Wilson estimate: 25.43 Å2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 4.16 / Num. unique all: 5772 / Rsym value: 0.399 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RT2

3rt2


Resolution: 2.113→32.499 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8629 / SU ML: 0.24 / σ(F): 0 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2848 5.1 %
Rwork0.173 --
obs0.1748 55874 95.24 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.02 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 203.27 Å2 / Biso mean: 36.291 Å2 / Biso min: 9.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.8226 Å2-0 Å25.357 Å2
2---3.7385 Å2-0 Å2
3---5.5611 Å2
Refinement stepCycle: LAST / Resolution: 2.113→32.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7592 0 2 507 8101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.027881
X-RAY DIFFRACTIONf_angle_d1.07410657
X-RAY DIFFRACTIONf_chiral_restr0.0711200
X-RAY DIFFRACTIONf_plane_restr0.0051382
X-RAY DIFFRACTIONf_dihedral_angle_d17.1212964
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1135-2.14990.2992780.21322090216874
2.1499-2.1890.24981420.20012431257389
2.189-2.23110.28651500.19952484263490
2.2311-2.27660.22081190.18332601272093
2.2766-2.32610.23381290.17962599272893
2.3261-2.38020.21881200.17912628274894
2.3802-2.43970.22461400.18762601274194
2.4397-2.50570.22061590.18992609276895
2.5057-2.57940.25461660.18912602276895
2.5794-2.66260.28261450.18582722286797
2.6626-2.75770.2241340.18222724285897
2.7577-2.86810.20641350.18442738287398
2.8681-2.99850.21921570.18342700285799
2.9985-3.15650.24071490.18432757290699
3.1565-3.3540.20721690.17652756292599
3.354-3.61270.18681460.169827852931100
3.6127-3.97570.15451590.154727792938100
3.9757-4.54960.18721400.143927952935100
4.5496-5.72690.17671580.147428042962100
5.7269-32.50310.18391530.18252821297498
Refinement TLS params.Method: refined / Origin x: 37.9109 Å / Origin y: 15.0621 Å / Origin z: 12.3016 Å
111213212223313233
T0.1137 Å2-0.0009 Å2-0.0106 Å2-0.0984 Å20.0132 Å2--0.1202 Å2
L0.3087 °2-0.0568 °2-0.1667 °2-0.1811 °20.1248 °2--0.1284 °2
S0.019 Å °-0.0173 Å °-0.0316 Å °0.0023 Å °0.0057 Å °-0.04 Å °-0.0187 Å °0.0088 Å °-0.0197 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA180 - 510
2X-RAY DIFFRACTION1allB180 - 506
3X-RAY DIFFRACTION1allC13 - 184
4X-RAY DIFFRACTION1allD19 - 184
5X-RAY DIFFRACTION1allA - C1 - 507
6X-RAY DIFFRACTION1allA - B1 - 512

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