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- PDB-5wxu: 11S globulin from Wrightia tinctoria reveals auxin binding site -

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Basic information

Entry
Database: PDB / ID: 5wxu
Title11S globulin from Wrightia tinctoria reveals auxin binding site
Components11S globulin
KeywordsPLANT PROTEIN / Auxin Natural Source
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls ...11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / 1H-INDOL-3-YLACETIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 11S globulin
Similarity search - Component
Biological speciesWrightia tinctoria (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKumar, P. / Kesari, P. / Dhindwal, S. / Kumar, P.
CitationJournal: Sci Rep / Year: 2017
Title: A novel function for globulin in sequestering plant hormone: Crystal structure of Wrightia tinctoria 11S globulin in complex with auxin.
Authors: Kumar, P. / Kesari, P. / Dhindwal, S. / Choudhary, A.K. / Katiki, M. / Verma, A. / Ambatipudi, K. / Tomar, S. / Sharma, A.K. / Mishra, G. / Kumar, P.
History
DepositionJan 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 11S globulin
B: 11S globulin
C: 11S globulin
D: 11S globulin
E: 11S globulin
F: 11S globulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,61545
Polymers323,0986
Non-polymers4,51739
Water37,7952098
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area66560 Å2
ΔGint-309 kcal/mol
Surface area62860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.209, 114.242, 202.479
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 , 1 types, 6 molecules ABCDEF

#1: Protein
11S globulin


Mass: 53849.656 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Wrightia tinctoria (plant) / References: UniProt: A0A162EGL7

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Non-polymers , 6 types, 2137 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID / Indole-3-acetic acid


Mass: 175.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H9NO2 / Comment: hormone*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2098 / 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 Å3/Da / Density meas: 2572802.25 Mg/m3 / Density % sol: 38.41 % / Description: Long rod-like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium citrate tribasic dihydrate, 100 mM Tris hydrochloride pH 8.5, 30% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→101.2 Å / Num. obs: 270464 / % possible obs: 94.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 17.63 Å2 / Rsym value: 0.068 / Net I/σ(I): 16.77
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.34 / Rsym value: 0.8 / % possible all: 92.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MxCuBEdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EHK

3ehk


Resolution: 1.7→101.24 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.766 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22718 13201 5 %RANDOM
Rwork0.17415 ---
obs0.17677 252210 94.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.74 Å2-0 Å2
3----1.65 Å2
Refinement stepCycle: 1 / Resolution: 1.7→101.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19049 0 282 2098 21429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01920303
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218435
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.96527609
X-RAY DIFFRACTIONr_angle_other_deg1.126342735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21152474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14223.6761042
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.172153386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.88515200
X-RAY DIFFRACTIONr_chiral_restr0.1850.22985
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02122788
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024216
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_it2.5422.3139795
X-RAY DIFFRACTIONr_mcbond_other2.5422.3139788
X-RAY DIFFRACTIONr_mcangle_it3.7273.43712270
X-RAY DIFFRACTIONr_mcangle_other3.7273.43712271
X-RAY DIFFRACTIONr_scbond_it3.7582.85710508
X-RAY DIFFRACTIONr_scbond_other3.7422.85410504
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6444.10415324
X-RAY DIFFRACTIONr_long_range_B_refined9.39330.32123451
X-RAY DIFFRACTIONr_long_range_B_other9.07529.46322780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 919 -
Rwork0.26 18124 -
obs--92.43 %

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