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- PDB-4ryv: Crystal structure of yellow lupin LLPR-10.1A protein in complex w... -

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Basic information

Entry
Database: PDB / ID: 4ryv
TitleCrystal structure of yellow lupin LLPR-10.1A protein in complex with trans-zeatin
ComponentsProtein LLPR-10.1A
KeywordsPLANT PROTEIN / PR-10 FOLD / LIGAND BINDING / PHYTOHORMONE BINDING PROTEIN / TRANS-ZEATIN / CYTOKININ
Function / homology
Function and homology information


cytokinin binding / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding ...cytokinin binding / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding / nucleus / cytosol
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / 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
(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / Protein LlR18A
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsDolot, R. / Michalska, K. / Sliwiak, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystallographic and CD probing of ligand-induced conformational changes in a plant PR-10 protein.
Authors: Sliwiak, J. / Dolot, R. / Michalska, K. / Szpotkowski, K. / Bujacz, G. / Sikorski, M. / Jaskolski, M.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein LLPR-10.1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9417
Polymers16,7491
Non-polymers1,1926
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein LLPR-10.1A
hetero molecules

A: Protein LLPR-10.1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,88214
Polymers33,4982
Non-polymers2,38512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1510 Å2
ΔGint-11.6 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.970, 63.910, 47.560
Angle α, β, γ (deg.)90.00, 126.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-487-

HOH

21A-519-

HOH

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Components

#1: Protein Protein LLPR-10.1A / LlPR10.1A


Mass: 16748.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Gene: LLR18A / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P52778
#2: Chemical
ChemComp-ZEA / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / TRANS-ZEATIN


Mass: 219.243 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H13N5O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8 M (NH4)2SO4, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0605
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 29, 2005
RadiationMonochromator: SINGLE ASYMMETRICALLY CUT SI(111) CRYSTAL WITH HORIZONTAL DIFFRACTION PLANE
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0605 Å / Relative weight: 1
ReflectionResolution: 1.38→99 Å / Num. obs: 34754 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.74
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 6.48 / % possible all: 99.6

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Processing

Software
NameVersionClassification
IS4CCDIdata collection
MOLREP10.2.31phasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ICX

1icx


Resolution: 1.38→42.49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.961 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17013 896 2.6 %RANDOM
Rwork0.142 ---
obs0.14274 33857 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.105 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-1.12 Å2
2---0.93 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.38→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 85 221 1489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191362
X-RAY DIFFRACTIONr_bond_other_d0.0010.021291
X-RAY DIFFRACTIONr_angle_refined_deg1.9872.0461852
X-RAY DIFFRACTIONr_angle_other_deg0.88833004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23126.15452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.7615231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.912151
X-RAY DIFFRACTIONr_chiral_restr0.1130.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211544
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02282
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_it1.4151.171645
X-RAY DIFFRACTIONr_mcbond_other1.411.169644
X-RAY DIFFRACTIONr_mcangle_it1.6331.774812
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5461.681717
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.78232652
X-RAY DIFFRACTIONr_sphericity_free45.271563
X-RAY DIFFRACTIONr_sphericity_bonded13.57152774
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 59 -
Rwork0.208 2482 -
obs--99.41 %

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