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- PDB-4hq1: Crystal structure of an LRR protein with two solenoids -

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Basic information

Entry
Database: PDB / ID: 4hq1
TitleCrystal structure of an LRR protein with two solenoids
ComponentsProbable receptor protein kinase TMK1
KeywordsTRANSFERASE / Receptor-like kinase
Function / homology
Function and homology information


transmembrane receptor protein serine/threonine kinase activity / membrane => GO:0016020 / non-specific serine/threonine protein kinase / signal transduction / extracellular region / ATP binding / nucleus / plasma membrane
Similarity search - Function
Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / 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 / Alpha Beta
Similarity search - Domain/homology
Receptor protein kinase TMK1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsChai, J. / Liu, P. / Hu, Z. / Zhou, B. / Liu, S.
CitationJournal: Cell Res. / Year: 2013
Title: Crystal structure of an LRR protein with two solenoids
Authors: Liu, P. / Hu, Z. / Zhou, B. / Liu, S. / Chai, J.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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_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_comp_id / _struct_ref_seq_dif.details
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: Probable receptor protein kinase TMK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5073
Polymers51,1881
Non-polymers1,3192
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.192, 50.511, 61.842
Angle α, β, γ (deg.)98.85, 108.74, 108.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Probable receptor protein kinase TMK1


Mass: 51187.660 Da / Num. of mol.: 1 / Fragment: UNP residues 1-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TMK1, At1g66150, F15E12.4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P43298, non-specific serine/threonine protein kinase
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 10

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG 3350, 0.15M NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2012
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: 1.55→50 Å / Num. all: 65335 / Num. obs: 62721 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.55→1.58 Å / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→27.707 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8872 / SU ML: 0.17 / σ(F): 1.97 / Phase error: 18.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 3172 5.06 %RANDOM
Rwork0.169 ---
all0.17 65335 --
obs0.17 62714 95.68 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.422 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 71.08 Å2 / Biso mean: 20.6795 Å2 / Biso min: 7.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.7339 Å21.6145 Å2-0.6363 Å2
2---0.2807 Å2-0.1571 Å2
3----0.4532 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 88 666 3968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043379
X-RAY DIFFRACTIONf_angle_d0.9874589
X-RAY DIFFRACTIONf_dihedral_angle_d12.9851264
X-RAY DIFFRACTIONf_chiral_restr0.062543
X-RAY DIFFRACTIONf_plane_restr0.004588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57310.29241220.24452364248687
1.5731-1.59770.25351290.21952571270095
1.5977-1.62390.24291310.21022587271894
1.6239-1.65190.21861330.19672548268195
1.6519-1.68190.26711440.19292575271995
1.6819-1.71430.21741360.18822558269495
1.7143-1.74920.24111430.18762583272695
1.7492-1.78730.19791400.17112588272896
1.7873-1.82880.20771460.17292550269696
1.8288-1.87460.19981530.16382598275196
1.8746-1.92520.21351190.17232598271796
1.9252-1.98190.19431260.16472605273196
1.9819-2.04580.18971330.16062644277796
2.0458-2.11890.17991320.15452597272996
2.1189-2.20370.16361470.15812605275297
2.2037-2.3040.19561460.16162636278297
2.304-2.42540.19571260.15952629275597
2.4254-2.57720.21081300.16492614274497
2.5772-2.7760.17911540.17132609276397
2.776-3.05510.19481500.17632633278397
3.0551-3.49640.19371310.16862589272096
3.4964-4.40230.16041380.14392606274496
4.4023-27.71120.16771630.18012655281899
Refinement TLS params.Method: refined / Origin x: 13.0006 Å / Origin y: 8.6827 Å / Origin z: -17.9414 Å
111213212223313233
T0.0929 Å2-0.005 Å2-0.003 Å2-0.0784 Å2-0.0114 Å2--0.0871 Å2
L0.2147 °2-0.2355 °20.2625 °2-0.3053 °2-0.3921 °2--0.4844 °2
S-0.0086 Å °-0.0019 Å °0.0149 Å °0.0352 Å °-0.0023 Å °-0.0067 Å °-0.0327 Å °0.0183 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 447
2X-RAY DIFFRACTION1allA1 - 507

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