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

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Basic information

Entry
Database: PDB / ID: 4jhh
TitleCrystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with kinetin
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 / 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
N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE / MALONATE ION / Nodulin-13
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Sep 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_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

Downloads & links

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Assembly

Deposited unit
A: MtN13 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1134
Polymers18,7731
Non-polymers3403
Water1,69394
1
A: MtN13 protein
hetero molecules

A: MtN13 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2278
Polymers37,5462
Non-polymers6806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area4020 Å2
ΔGint-25 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.415, 96.415, 113.407
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-336-

HOH

21A-367-

HOH

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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-H35 / N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE


Mass: 215.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9N5O / Comment: hormone*YM
#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.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 4.05 Å3/Da / Density % sol: 69.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.85 M SODIUM MALONATE, 200 mM NaCl, 50 mM Tris-HCl, protein was incubated overnight with kinetin 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: BESSY / Beamline: 14.1 / Wavelength: 0.91801 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2012 / Details: focusing mirrors
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91801 Å / Relative weight: 1
ReflectionResolution: 2.2→48.22 Å / Num. all: 16457 / Num. obs: 16292 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 41.508 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.49
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.2-2.330.6471.96120332433194.4
2.33-2.490.5023.051506124481100
2.49-2.690.3394.6138942274199.9
2.69-2.940.2097.71128732110199.9
2.94-3.290.10214.581171519281100
3.29-3.80.05625.58103131720199.9
3.8-4.640.0435.2787311477199.8
4.64-6.540.03835.9367081181199.9
6.54-48.220.02642.193671721198.8

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Processing

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

3rws
PDB Unreleased entry


Resolution: 2.2→48.22 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.24 / Cross valid method: R-free / Phase error: 22.32 / Stereochemistry target values: Engh & Huber / Details: Hydrogen atoms were added at riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 1002 6.15 %random
Rwork0.1858 ---
all0.1876 16292 --
obs0.1876 16286 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.41 Å2 / Biso mean: 50.4 Å2 / Biso min: 23.74 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 24 94 1400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021347
X-RAY DIFFRACTIONf_angle_d1.7251824
X-RAY DIFFRACTIONf_chiral_restr0.095197
X-RAY DIFFRACTIONf_plane_restr0.009234
X-RAY DIFFRACTIONf_dihedral_angle_d24.437827
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.310.31271310.26791999213094
2.31-2.460.26021410.244721612302100
2.46-2.650.28231410.228121482289100
2.65-2.910.29721430.224921832326100
2.91-3.340.23041440.188121962340100
3.34-4.20.161460.14822302376100
4.2-48.220.18161560.161823672523100
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)
15.0743-2.74271.06783.4495-0.24012.7364-0.01190.34690.2622-0.1709-0.15560.1588-0.4801-0.44420.15210.35570.0385-0.0160.3337-0.0040.292433.55212.59742.7216
26.7274-1.3856-2.5125.48043.42064.56360.15280.14710.4284-0.1911-0.1512-0.0163-0.7924-0.4585-0.06390.46830.1623-0.08720.31360.0450.306935.63225.55714.8351
31.83840.101-0.25434.02781.13932.5555-0.08260.01750.0264-0.03460.1640.1399-0.4264-0.2343-0.02330.31940.1027-0.01420.30510.03380.277438.11619.09013.4958
48.72441.94643.21464.18792.24915.1177-0.1732-0.6154-0.2460.30920.3155-0.1573-0.21960.0653-0.12770.33220.08850.04960.27770.03330.267542.837911.09718.9256
58.6067-0.3783.34276.0651-0.59956.726-0.3755-0.1991-0.23320.2930.20560.0675-0.4137-0.24540.17670.26550.0170.08940.1855-0.04410.275138.31895.03317.2144
69.4669-3.16331.95757.6197-0.02275.0283-0.4006-0.31760.2960.76110.26950.4285-0.3026-0.5750.25920.35350.07970.02810.3877-0.10570.376327.529113.76378.7697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID -3:34 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 35:53 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 54:84 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 85:106 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 107:130 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 131:158 )A0

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