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- PDB-5y92: Crystal structure of ANXUR2 extracellular domain from Arabidopsis... -

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Basic information

Entry
Database: PDB / ID: 5y92
TitleCrystal structure of ANXUR2 extracellular domain from Arabidopsis thaliana
ComponentsReceptor-like protein kinase ANXUR2
KeywordsTRANSFERASE / receptor-like kinases
Function / homology
Function and homology information


pollen tube tip / plasmodesma / transmembrane receptor protein tyrosine kinase activity / non-specific serine/threonine protein kinase / apical plasma membrane / phosphorylation / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / SAD / Resolution: 2.004 Å
AuthorsDu, S. / Xiao, J.Y.
CitationJournal: Protein Sci. / Year: 2018
Title: Crystal structures of the extracellular domains of the CrRLK1L receptor-like kinases ANXUR1 and ANXUR2
Authors: Du, S. / Qu, L.J. / Xiao, J.
History
DepositionAug 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,6375
Polymers42,8181
Non-polymers1,8194
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint29 kcal/mol
Surface area18210 Å2
Unit cell
Length a, b, c (Å)103.189, 103.189, 121.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Receptor-like protein kinase ANXUR2


Mass: 42817.977 Da / Num. of mol.: 1 / Fragment: UNP residues 28-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ANX2, At5g28680, F4I4.60 / Production host: Trichoplusia ni ascovirus 2a
References: UniProt: Q3E8W4, non-specific serine/threonine protein kinase
#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.: 2 / Source method: obtained synthetically
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: obtained synthetically
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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.64 Å3/Da / Density % sol: 66.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M li2SO4 ,0.1M NaAc (pH=4.5), 50% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42707 / % possible obs: 100 % / Redundancy: 13.3 % / Net I/σ(I): 34.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.004→43.151 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.18
RfactorNum. reflection% reflection
Rfree0.208 1982 4.66 %
Rwork0.1836 --
obs0.1847 42522 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.004→43.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 0 105 3240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093221
X-RAY DIFFRACTIONf_angle_d1.0874401
X-RAY DIFFRACTIONf_dihedral_angle_d12.9831908
X-RAY DIFFRACTIONf_chiral_restr0.062511
X-RAY DIFFRACTIONf_plane_restr0.006561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.004-2.05410.33561390.26532849X-RAY DIFFRACTION98
2.0541-2.10960.25931440.22362878X-RAY DIFFRACTION99
2.1096-2.17170.24621420.21372850X-RAY DIFFRACTION99
2.1717-2.24180.25921410.20812881X-RAY DIFFRACTION99
2.2418-2.32190.26171390.20462879X-RAY DIFFRACTION100
2.3219-2.41490.24591400.20962888X-RAY DIFFRACTION100
2.4149-2.52480.2161480.20062908X-RAY DIFFRACTION100
2.5248-2.65790.26791360.20522890X-RAY DIFFRACTION100
2.6579-2.82440.24541400.21012875X-RAY DIFFRACTION100
2.8244-3.04240.26091430.21232929X-RAY DIFFRACTION100
3.0424-3.34850.22021470.2082910X-RAY DIFFRACTION100
3.3485-3.83270.20041420.18032916X-RAY DIFFRACTION100
3.8327-4.82780.17871340.14432927X-RAY DIFFRACTION100
4.8278-43.16120.16161470.1682960X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.4077 Å / Origin y: 26.7007 Å / Origin z: 73.8147 Å
111213212223313233
T0.3243 Å2-0.0388 Å2-0.0241 Å2-0.3164 Å2-0.0268 Å2--0.3195 Å2
L2.5479 °20.5802 °2-2.0016 °2-0.7642 °2-0.5877 °2--3.1346 °2
S0.0758 Å °-0.0857 Å °0.0747 Å °0.002 Å °-0.0313 Å °-0.0492 Å °-0.1283 Å °0.2954 Å °-0.0625 Å °
Refinement TLS groupSelection details: all

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