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- PDB-4gy9: Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in co... -

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Basic information

Entry
Database: PDB / ID: 4gy9
TitleCrystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with N6-isopentenyladenine (2iP)
ComponentsMtN13 protein
KeywordsPLANT PROTEIN / PR-10 FOLD / nodulin / nodulation / legume plant-rhizobium symbiosis / 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 / nucleus / cytoplasm
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
MALONATE ION / N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE / Nodulin-13
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 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: 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.
#2: 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.
#3: 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.
#4: Journal: J.Struct.Biol. / Year: 2010
Title: Crystal structure of Hyp-1, a St. John's wort protein implicated in the biosynthesis of hypericin.
Authors: Michalska, K. / Fernandes, H. / Sikorski, M. / Jaskolski, M.
#5: Journal: Mol.Plant Microbe Interact. / Year: 1996
Title: Use of a subtractive hybridization approach to identify new Medicago truncatula genes induced during root nodule development.
Authors: Gamas, P. / Niebel Fde, C. / Lescure, N. / Cullimore, J.
#6: 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.
#7: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of two homologous pathogenesis-related proteins from yellow lupine.
Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Dec 3, 2014Group: Data collection
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Sep 13, 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 / pdbx_struct_conn_angle / 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.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_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

Downloads & links

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Assembly

Deposited unit
A: MtN13 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2169
Polymers18,7731
Non-polymers4438
Water2,630146
1
A: MtN13 protein
hetero molecules

A: MtN13 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,43318
Polymers37,5462
Non-polymers88616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area5350 Å2
ΔGint-125 kcal/mol
Surface area15950 Å2
MethodPISA
2
A: MtN13 protein
hetero molecules

A: MtN13 protein
hetero molecules

A: MtN13 protein
hetero molecules

A: MtN13 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,86536
Polymers75,0924
Non-polymers1,77332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area13460 Å2
ΔGint-254 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.596, 96.596, 112.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21A-438-

HOH

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Components

#1: Protein MtN13 protein / Uncharacterized protein


Mass: 18773.020 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-ZIP / N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE / ISOPENTENYLADENINE


Mass: 203.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 4.02 Å3/Da / Density % sol: 69.39 %
Crystal growTemperature: 292 K / pH: 7.1
Details: 1.5 M sodium malonate, Dehydration at elevated sodium malonate concentration (1.9 M), pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.22343
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 31, 2012
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22343 Å / Relative weight: 1
ReflectionNumber: 287179 / Rmerge(I) obs: 0.099 / D res high: 2.036 Å / Num. obs: 20324 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
6.065088999.410.029
4.36.06145510010.034
3.524.3183110010.045
3.053.52212710010.066
2.733.05239610010.12
2.492.73260710010.208
2.312.49283810010.302
2.162.31303210010.44
2.0362.16314998.210.706
ReflectionResolution: 2.04→50 Å / Num. obs: 20324 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 24.33
Reflection shellResolution: 2.04→2.16 Å / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 3.95 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å48.3 Å
Translation2.5 Å48.3 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RWS

3rws
PDB Unreleased entry


Resolution: 2.04→48.3 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.16 / Phase error: 18.33 / Stereochemistry target values: ENGH & HUBER / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.198 1004 4.94 %
Rwork0.165 --
obs0.167 20321 99.7 %
all-20321 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.05 Å2
Refinement stepCycle: LAST / Resolution: 2.04→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 28 146 1456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191384
X-RAY DIFFRACTIONf_angle_d1.4091894
X-RAY DIFFRACTIONf_dihedral_angle_d15.198507
X-RAY DIFFRACTIONf_chiral_restr0.08198
X-RAY DIFFRACTIONf_plane_restr0.008236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.1430.23691370.19072650X-RAY DIFFRACTION98
2.143-2.2770.22071400.15972690X-RAY DIFFRACTION100
2.277-2.4530.21581420.16012723X-RAY DIFFRACTION100
2.453-2.70.21961410.17122731X-RAY DIFFRACTION100
2.7-3.090.21081440.17512754X-RAY DIFFRACTION100
3.09-3.8930.17621450.14552803X-RAY DIFFRACTION100
3.893-48.3120.18411550.172966X-RAY DIFFRACTION100
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)
19.509-1.42211.03571.3498-0.11371.163-0.09640.12660.00340.14410.0572-0.0804-0.08320.06430.05290.2316-0.0118-0.01040.1568-0.00210.217345.41922.25998.4346
27.60842.94160.05954.57611.85342.0914-0.34160.38510.2756-0.62150.16530.7069-0.1576-0.3148-0.01060.3130.0624-0.09010.3478-0.01530.349225.125215.6064-4.3176
31.30970.0196-0.40671.11930.68251.3134-0.00590.0990.1412-0.187-0.03740.1257-0.2063-0.17670.05860.28610.0603-0.0110.19580.01810.205235.670523.9135.4646
43.0785-0.14690.7582.01030.48892.3231-0.07870.0462-0.1394-0.09920.06420.149-0.1103-0.0707-0.00020.19580.02460.01250.13110.00540.181237.97349.62034.0954
53.3762-0.64481.02912.4725-0.29541.813-0.3175-0.06290.18630.40990.0234-0.0343-0.1101-0.01570.28540.24520.03730.00470.2236-0.04280.211333.055211.005211.2028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID -4:12)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 13:24)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 25:74)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 75:122)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 123:158)

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