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- PDB-4jhi: Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in co... -

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Basic information

Entry
Database: PDB / ID: 4jhi
TitleCrystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with N6-benzyladenine
ComponentsMtN13 protein
KeywordsPLANT PROTEIN / PR-10 FOLD / nodulin / nodulation / legume-bacteria symbiosis / nitrogen fixation / CYTOKININ BINDING
Function / homology
Function and homology information


nodulation / cytokinin-activated signaling pathway / response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
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
N-BENZYL-9H-PURIN-6-AMINE / Nodulin-13
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRuszkowski, M. / Sikorski, M. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The landscape of cytokinin binding by a plant nodulin.
Authors: Ruszkowski, M. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M.
#1: Journal: Febs J. / Year: 2013
Title: Structural and functional aspects of PR-10 proteins.
Authors: Fernandes, H. / Michalska, K. / Sikorski, M. / Jaskolski, M.
#2: Journal: J.Mol.Biol. / Year: 2008
Title: Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin.
Authors: Fernandes, H. / Pasternak, O. / Bujacz, G. / Bujacz, A. / Sikorski, M.M. / Jaskolski, M.
#3: Journal: Febs J. / Year: 2009
Title: Cytokinin-induced structural adaptability of a Lupinus luteus PR-10 protein.
Authors: Fernandes, H. / Bujacz, A. / Bujacz, G. / Jelen, F. / Jasinski, M. / Kachlicki, P. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#4: Journal: Plant Cell / Year: 2006
Title: Crystal structure of Vigna radiata cytokinin-specific binding protein in complex with zeatin.
Authors: Pasternak, O. / Bujacz, G.D. / Fujimoto, Y. / Hashimoto, Y. / Jelen, F. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#5: Journal: Mol.Plant Microbe Interact. / Year: 1998
Title: Symbiosis-specific expression of two Medicago truncatula nodulin genes, MtN1 and MtN13, encoding products homologous to plant defense proteins.
Authors: Gamas, P. / de Billy, F. / Truchet, G.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Data collection / Refinement description
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / 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_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_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_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

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Assembly

Deposited unit
A: MtN13 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9083
Polymers18,6601
Non-polymers2482
Water45025
1
A: MtN13 protein
hetero molecules

A: MtN13 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8166
Polymers37,3202
Non-polymers4964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area3720 Å2
ΔGint-27 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.086, 96.086, 113.584
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

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Components

#1: Protein MtN13 protein


Mass: 18659.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MtN13 / Plasmid: PET TOPO 151D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: P93330
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EMU / N-BENZYL-9H-PURIN-6-AMINE / BENZYLAMINOPURINE / 6-Benzylaminopurine


Mass: 225.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N5 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.06 Å3/Da / Density % sol: 69.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.7 M SODIUM MALONATE, 200 mM NaCl, 50 mM Tris-HCl, protein was incubated overnight with N6-benzylopurine prior to crystallization, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04172 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2012 / Details: Sagitally focusing multilayer mirror
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04172 Å / Relative weight: 1
ReflectionResolution: 2.6→46.9 Å / Num. all: 10040 / Num. obs: 10018 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.760.6844.33167851568199.6
2.76-2.950.4346.64157791461199.9
2.95-3.180.2669.91499513961100
3.18-3.480.15815.991377012921100
3.48-3.890.10621.881230911621100
3.89-4.490.07628.031107410611100
4.49-5.490.06531.129188901199.9
5.49-7.710.08226.117206726199.7
7.71-46.90.04738.053908451197.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3rws

3rws
PDB Unreleased entry


Resolution: 2.6→46.9 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.25 / Cross valid method: R-free / Phase error: 21.14 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 802 8.01 %Random
Rwork0.1704 ---
all0.1747 10040 --
obs0.1747 10017 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.13 Å2 / Biso mean: 39.4 Å2 / Biso min: 8.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 18 25 1317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151323
X-RAY DIFFRACTIONf_angle_d1.6141787
X-RAY DIFFRACTIONf_chiral_restr0.095194
X-RAY DIFFRACTIONf_plane_restr0.007229
X-RAY DIFFRACTIONf_dihedral_angle_d17.302487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.760.34041300.242514871617100
2.76-2.980.2891290.223714921621100
2.98-3.280.2471310.195215041635100
3.28-3.750.22811320.15815231655100
3.75-4.720.18941350.131815511686100
4.72-46.90.191450.16321658180399

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