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- PDB-6fih: Crystal structure of the ANX2 ectodomain from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 6fih
TitleCrystal structure of the ANX2 ectodomain from Arabidopsis thaliana
ComponentsReceptor-like protein kinase ANXUR2
KeywordsPLANT PROTEIN / receptor kinase / malectin-like domain / membrane protein / Arabidopsis thaliana
Function / homology
Function and homology information


pollen tube tip / transmembrane receptor protein tyrosine kinase activity / non-specific serine/threonine protein kinase / apical plasma membrane / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Malectin-like domain / Receptor-like protein kinase ANXUR1-like / Malectin-like domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-like protein kinase ANXUR2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.08 Å
AuthorsSantiago, J.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
European Research CouncilWallWatchers 716358 Switzerland
Swiss National Science Foundation31003A_173101 Switzerland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystal structures of two tandem malectin-like receptor kinases involved in plant reproduction.
Authors: Moussu, S. / Augustin, S. / Roman, A.O. / Broyart, C. / Santiago, J.
History
DepositionJan 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_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_asym_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-like protein kinase ANXUR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,55711
Polymers45,7751
Non-polymers1,78210
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint36 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.566, 41.766, 93.371
Angle α, β, γ (deg.)90.00, 117.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1019-

HOH

21A-1028-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Receptor-like protein kinase ANXUR2


Mass: 45775.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ANX2, At5g28680, F4I4.60 / Cell line (production host): Tnaos38 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q3E8W4, non-specific serine/threonine protein kinase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 439 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999894 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999894 Å / Relative weight: 1
ReflectionResolution: 1.08→44.29 Å / Num. obs: 175203 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 6.46 % / Biso Wilson estimate: 17.9 Å2 / CC1/2: 1 / Rrim(I) all: 0.04 / Rsym value: 0.037 / Net I/σ(I): 18.94
Reflection shellResolution: 1.08→1.15 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.17 / Num. unique obs: 25949 / CC1/2: 0.59 / Rrim(I) all: 1.29 / Rsym value: 1.16 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.08→44.29 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.454 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18269 8689 5 %RANDOM
Rwork0.15911 ---
obs0.16029 165089 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20.88 Å2
2---2.3 Å20 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.08→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 113 433 3496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023233
X-RAY DIFFRACTIONr_bond_other_d0.0030.022903
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9944426
X-RAY DIFFRACTIONr_angle_other_deg1.04536812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5685409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81725138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.24115513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6071511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213559
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02624
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_it1.6942.0661549
X-RAY DIFFRACTIONr_mcbond_other1.6862.0641548
X-RAY DIFFRACTIONr_mcangle_it2.1173.111942
X-RAY DIFFRACTIONr_mcangle_other2.1233.1111943
X-RAY DIFFRACTIONr_scbond_it2.312.3441684
X-RAY DIFFRACTIONr_scbond_other2.312.3431684
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6933.432470
X-RAY DIFFRACTIONr_long_range_B_refined3.91127.4543671
X-RAY DIFFRACTIONr_long_range_B_other3.43626.4423562
X-RAY DIFFRACTIONr_rigid_bond_restr2.73636136
X-RAY DIFFRACTIONr_sphericity_free34.5055275
X-RAY DIFFRACTIONr_sphericity_bonded14.46656202
LS refinement shellResolution: 1.081→1.109 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.535 503 -
Rwork0.542 9560 -
obs--75.65 %

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