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- PDB-3njo: X-ray crystal structure of the Pyr1-pyrabactin A complex -

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Basic information

Entry
Database: PDB / ID: 3njo
TitleX-ray crystal structure of the Pyr1-pyrabactin A complex
ComponentsAbscisic acid receptor PYR1
KeywordsHORMONE RECEPTOR / START / ABA / PYR/PYL/RCAR / plant hormone / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


positive regulation of response to water deprivation / regulation of protein serine/threonine phosphatase activity / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity ...positive regulation of response to water deprivation / regulation of protein serine/threonine phosphatase activity / plant-type vacuole membrane / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Polyketide cyclase / dehydrase and lipid transport / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Chem-PYV / Abscisic acid receptor PYR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.473 Å
AuthorsBurgie, E.S. / Bingman, C.A. / Phillips Jr., G.N. / Peterson, F.C. / Volkman, B.F. / Cutler, S.R. / Jensen, D.R. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis for selective activation of ABA receptors.
Authors: Peterson, F.C. / Burgie, E.S. / Park, S.Y. / Jensen, D.R. / Weiner, J.J. / Bingman, C.A. / Chang, C.E. / Cutler, S.R. / Phillips, G.N. / Volkman, B.F.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 6, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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_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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Abscisic acid receptor PYR1
C: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,93010
Polymers65,6263
Non-polymers1,3037
Water1,22568
1
A: Abscisic acid receptor PYR1
B: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5817
Polymers43,7512
Non-polymers8305
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-42 kcal/mol
Surface area18370 Å2
MethodPISA
2
C: Abscisic acid receptor PYR1
hetero molecules

C: Abscisic acid receptor PYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6986
Polymers43,7512
Non-polymers9474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area1890 Å2
ΔGint-39 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.307, 60.307, 527.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-211-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 21875.486 Da / Num. of mol.: 3 / Mutation: P88S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: ABIP6, At4g17870, PYR1, RCAR11, T6K21.50 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O49686

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Non-polymers , 6 types, 75 molecules

#2: Chemical ChemComp-PYV / 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Pyrabactin


Mass: 377.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13BrN2O2S / Comment: hormone*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-P2M / N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide


Mass: 298.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O2S
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein solution 100 nl- 20 mM NaCl, 2 mM DTT 20 mM Tris, pH 7.6, Precipitant solution 100 nl- 2.0 M ammonium sulfate, 100 mM BisTris, pH 5.5, Cryoprotectant- Fomblin 06/6, VAPOR DIFFUSION, ...Details: Protein solution 100 nl- 20 mM NaCl, 2 mM DTT 20 mM Tris, pH 7.6, Precipitant solution 100 nl- 2.0 M ammonium sulfate, 100 mM BisTris, pH 5.5, Cryoprotectant- Fomblin 06/6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionRedundancy: 5.4 % / Av σ(I) over netI: 13.62 / Number: 113045 / Rmerge(I) obs: 0.086 / Χ2: 0.93 / D res high: 2.47 Å / D res low: 50 Å / Num. obs: 21108 / % possible obs: 95.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.75087.810.0320.7834.4
5.326.788.710.040.8994.7
4.655.3290.610.0360.8964.8
4.224.6592.910.0420.8795
3.924.2293.510.0520.9125.1
3.693.929310.080.734.8
3.53.6988.810.1280.8354.4
3.353.596.510.0990.6835.2
3.223.3597.610.1070.9475.5
3.113.2299.110.1270.9635.7
3.013.1197.610.1361.0175.9
2.933.0199.510.1631.046
2.852.9397.710.2171.016.2
2.782.8599.710.2631.0416.2
2.722.7897.710.3321.0356.2
2.662.7299.410.3950.9156
2.612.6699.510.4660.8525.8
2.562.6198.510.5271.035.5
2.512.5699.310.5660.9745.2
2.472.5193.110.5090.974.4
ReflectionResolution: 2.47→50 Å / Num. obs: 21108 / % possible obs: 95.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.086 / Χ2: 0.929 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.47-2.514.40.50910180.9793.1
2.51-2.565.20.56610160.97499.3
2.56-2.615.50.52710731.0398.5
2.61-2.665.80.46610290.85299.5
2.66-2.7260.39510690.91599.4
2.72-2.786.20.33210381.03597.7
2.78-2.856.20.26310861.04199.7
2.85-2.936.20.21710241.0197.7
2.93-3.0160.16311081.0499.5
3.01-3.115.90.13610261.01797.6
3.11-3.225.70.12710610.96399.1
3.22-3.355.50.10711000.94797.6
3.35-3.55.20.09910360.68396.5
3.5-3.694.40.1289700.83588.8
3.69-3.924.80.0810270.7393
3.92-4.225.10.05210500.91293.5
4.22-4.6550.04210650.87992.9
4.65-5.324.80.03610460.89690.6
5.32-6.74.70.0410690.89988.7
6.7-504.40.03211970.78387.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3JRS, subunit A only

3jrs


Resolution: 2.473→32.046 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.36 / σ(F): 0.1 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 1882 9.55 %random
Rwork0.2218 ---
obs0.226 19707 89.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.552 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso max: 195.49 Å2 / Biso mean: 54.958 Å2 / Biso min: 2.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.6398 Å20 Å2-0 Å2
2--5.6398 Å20 Å2
3----11.2797 Å2
Refinement stepCycle: LAST / Resolution: 2.473→32.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4156 0 77 68 4301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0264403
X-RAY DIFFRACTIONf_angle_d1.5725968
X-RAY DIFFRACTIONf_chiral_restr0.13667
X-RAY DIFFRACTIONf_plane_restr0.01757
X-RAY DIFFRACTIONf_dihedral_angle_d17.9511615
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.473-2.53990.35771210.29511167128878
2.5399-2.61460.3481310.2661257138884
2.6146-2.69890.34031360.27831253138988
2.6989-2.79530.32561440.25281347149190
2.7953-2.90720.31391470.24451381152893
2.9072-3.03940.28021500.22231416156695
3.0394-3.19950.27421510.2271443159496
3.1995-3.39970.27391510.22111426157795
3.3997-3.66190.23911400.20581325146589
3.6619-4.02980.24681450.1991384152988
4.0298-4.61140.19031530.15981433158693
4.6114-5.80430.22481480.18841426157489
5.8043-32.04910.27551650.25281567173289
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)
11.8986-0.12350.27841.628-0.84483.12370.12830.2237-0.00570.18890.0471-0.08-0.0420.1539-0.13240.1320.0258-0.00830.2115-0.02260.092210.8608-15.119914.2856
21.6715-0.2208-0.7481.12090.21194.03670.0050.05260.02260.0513-0.05660.00390.1202-0.47070.05580.076-0.10260.02380.2893-0.02050.0987-16.3765-3.630215.0198
31.4471-0.1718-0.19181.82660.02964.67230.0153-0.07610.0474-0.01180.024-0.12440.13980.1307-0.02430.05040.05760.02420.130.00340.110916.6913-7.24645.0031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:300)A6 - 300
2X-RAY DIFFRACTION2(chain B and resid 4:300)B4 - 300
3X-RAY DIFFRACTION3(chain C and resid 3:300)C3 - 300

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