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

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Basic information

Entry
Database: PDB / ID: 4jhg
TitleCrystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with trans-zeatin
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 / 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
MALONATE ION / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / Nodulin-13
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRuszkowski, M. / Tusnio, K. / Ciesielska, A. / Brzezinski, K. / Dauter, M. / Dauter, Z. / 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
SupersessionMar 20, 2013ID: 3RWS
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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 / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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)19,1636
Polymers18,7731
Non-polymers3905
Water2,180121
1
A: MtN13 protein
hetero molecules

A: MtN13 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,32712
Polymers37,5462
Non-polymers78110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area4590 Å2
ΔGint-81 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.110, 96.110, 113.244
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein MtN13 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-ZEA / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / TRANS-ZEATIN


Mass: 219.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 69.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.9 M SODIUM MALONATE, 200 mM NaCl, 50 mM Tris-HCl, protein was incubated overnight with trans-zeatin 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: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2011 / Details: FOCUSING MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 26897 / Num. obs: 26831 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.075 / Χ2: 1.092 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.85-1.928.90.9812.126271.118100
1.92-1.9910.40.8043.726261.106100
1.99-2.0810.80.525.726411.117100
2.08-2.1910.80.3738.326431.129100
2.19-2.3310.90.24512.426451.119100
2.33-2.5110.80.18315.426801100
2.51-2.7610.80.12421.126740.984100
2.76-3.1610.80.07430.627000.943100
3.16-3.9810.60.06635.227451.26199.9
3.98-309.90.03552.629161.14999.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2qim

2qim


Resolution: 1.85→24.92 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.16 / Cross valid method: R-free / Phase error: 21.92 / Stereochemistry target values: Engh & Huber / Details: Hydrogen atoms were added at riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1349 5.03 %random
Rwork0.182 ---
obs0.1837 26803 99.72 %-
all-26831 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.28 Å2 / Biso mean: 47.6 Å2 / Biso min: 20.67 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 26 121 1429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191372
X-RAY DIFFRACTIONf_angle_d1.5781861
X-RAY DIFFRACTIONf_chiral_restr0.095202
X-RAY DIFFRACTIONf_plane_restr0.011238
X-RAY DIFFRACTIONf_dihedral_angle_d15.988516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.920.27911230.2532482260599
1.92-20.23931140.224424972611100
2-2.090.24691280.207325002628100
2.09-2.20.20191490.189424852634100
2.2-2.330.22081360.187825032639100
2.33-2.510.26071450.190325232668100
2.51-2.770.25351450.206925272672100
2.77-3.170.24491410.19925552696100
3.17-3.990.18151280.162826192747100
3.99-24.920.19311400.164427632903100
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)
13.9787-2.73314.02913.747-1.24515.2407-0.1671-0.0482-0.05140.26930.1541-0.204-0.0655-0.0202-0.00220.31710.00560.01470.1414-0.02890.319344.38362.59448.102
25.27641.1664-2.42288.79332.55224.0054-0.17540.47740.0582-0.73930.18380.6132-0.7763-0.4610.02980.45820.1868-0.14210.4380.02570.435526.499819.6073-1.0304
32.7271-1.4368-1.79313.662.39785.1657-0.0593-0.03950.2302-0.11810.11540.0652-0.5594-0.2488-0.08450.42680.122-0.01960.23570.03240.28337.457523.19515.89
48.28071.28563.45183.73091.89745.3328-0.3532-0.0982-0.0720.03940.23650.2143-0.3296-0.09890.07920.26940.06980.05580.12250.03970.215840.948311.99265.5839
50.04150.38320.07263.84330.95891.0591-0.2137-0.1168-0.4792-0.2080.1380.7077-0.2831-0.54730.0650.28690.0221-0.00090.35870.03850.432131.95.62561.7274
68.1938-4.0523.71414.8301-2.14523.4102-0.12340.23080.04290.4036-0.11020.0337-0.07960.05150.2430.48430.0667-0.00070.3654-0.06460.369232.326811.593110.5159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID -4:12 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 13:34 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 35:74 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 75:106 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 107:122 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 123:158 )A0

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