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- PDB-4oic: Crystal structrual of a soluble protein -

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Basic information

Entry
Database: PDB / ID: 4oic
TitleCrystal structrual of a soluble protein
Components
  • Bet v I allergen-like
  • Probable protein phosphatase 2C 6
KeywordsHORMONE RECEPTOR/HYDROLASE / START fold / PYL-phosphatases complex / ABA signaling pathway / HORMONE RECEPTOR-HYDROLASE complex
Function / homology
Function and homology information


regulation of intracellular signal transduction / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein serine/threonine phosphatase activity / protein phosphatase inhibitor activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity ...regulation of intracellular signal transduction / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein serine/threonine phosphatase activity / protein phosphatase inhibitor activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / response to cold / signaling receptor activity / protein homodimerization activity / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sigma factor PP2C-like phosphatases / 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 ...Sigma factor PP2C-like phosphatases / 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 / : / Probable protein phosphatase 2C 6 / Abscisic acid receptor PYL9
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsHe, Y. / Hao, Q. / Li, W. / Yan, C. / Yan, N. / Yin, P.
CitationJournal: Plos One / Year: 2014
Title: Identification and characterization of ABA receptors in Oryza sativa
Authors: He, Y. / Hao, Q. / Li, W. / Yan, C. / Yan, N. / Yin, P.
History
DepositionJan 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_seq_id / _struct_conn.ptnr2_label_asym_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: Bet v I allergen-like
B: Probable protein phosphatase 2C 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5909
Polymers71,0472
Non-polymers5437
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-11 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.190, 43.522, 73.994
Angle α, β, γ (deg.)90.00, 92.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-504-

MN

21B-505-

NA

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Bet v I allergen-like / OsPYL2


Mass: 22360.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os06g0562200 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5Z8S0
#2: Protein Probable protein phosphatase 2C 6 / OsPP2C06


Mass: 48686.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os01g0583100 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0JLP9, protein-serine/threonine phosphatase

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Non-polymers , 5 types, 455 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 / Comment: hormone*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 1.86 Å3/Da / Density % sol: 33.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, 0.2M MgCl2, 20% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. all: 35816 / Num. obs: 34921 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 20.78 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 88.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KDH and 3KDJ

3kdh

3kdj


Resolution: 1.999→36.74 Å / FOM work R set: 0.875 / SU ML: 0.19 / σ(F): 1.35 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 1742 4.99 %RANDOM
Rwork0.1699 ---
all0.1715 35816 --
obs0.1715 34912 97.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.66 Å2 / Biso mean: 34.46 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: LAST / Resolution: 1.999→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3729 0 25 448 4202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083843
X-RAY DIFFRACTIONf_angle_d1.1755224
X-RAY DIFFRACTIONf_chiral_restr0.047594
X-RAY DIFFRACTIONf_plane_restr0.004683
X-RAY DIFFRACTIONf_dihedral_angle_d14.5081405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9987-2.05750.26251180.23692461257987
2.0575-2.12390.2521460.21232631277795
2.1239-2.19980.23781500.19742748289898
2.1998-2.28790.22941470.19282793294099
2.2879-2.3920.2221500.18892778292899
2.392-2.5180.21331230.184228212944100
2.518-2.67580.2321450.17612814295999
2.6758-2.88230.23181540.17472819297399
2.8823-3.17220.20281490.175728282977100
3.1722-3.63090.19261330.15592832296599
3.6309-4.57310.16121690.13782821299099
4.5731-36.74660.17211580.15192824298296
Refinement TLS params.Method: refined / Origin x: -3.7148 Å / Origin y: 0.8663 Å / Origin z: 55.1284 Å
111213212223313233
T0.1022 Å20.0064 Å20.0102 Å2-0.1563 Å20.014 Å2--0.0819 Å2
L0.4755 °20.1152 °20.0881 °2-0.8732 °20.0931 °2--1.6549 °2
S-0.007 Å °-0.0011 Å °0.0484 Å °0.0472 Å °0.044 Å °0.0108 Å °0.0173 Å °-0.3502 Å °-0.0201 Å °
Refinement TLS groupSelection details: ALL

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