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- PDB-5uv4: Crystal Structure of Maize SIRK1 (sucrose-induced receptor kinase... -

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Basic information

Entry
Database: PDB / ID: 5uv4
TitleCrystal Structure of Maize SIRK1 (sucrose-induced receptor kinase 1) kinase domain bound to AMP-PNP
ComponentsPutative leucine-rich repeat protein kinase family protein
KeywordsTRANSFERASE / receptor-like kinase / leucine-rich repeat / sucrose-induced kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


membrane => GO:0016020 / protein kinase activity / ATP binding
Similarity search - Function
Leucine Rich repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Putative leucine-rich repeat protein kinase family protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCounago, R.M. / Aquino, B. / Massirer, K.B. / Gileadi, O. / Arruda, P. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of Maize SIRK1 (sucrose-induced receptor kinase 1) kinase domain bound to AMP-PNP
Authors: Aquino, B. / Counago, R.M. / Massirer, K.B. / Gileadi, O. / Arruda, P. / Structural Genomics Consortium (SGC)
History
DepositionFeb 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative leucine-rich repeat protein kinase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0293
Polymers34,4981
Non-polymers5312
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.444, 74.532, 79.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative leucine-rich repeat protein kinase family protein /


Mass: 34498.344 Da / Num. of mol.: 1 / Fragment: UNP residues 737-1045
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ZEAMMB73_708518 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 R3 / References: UniProt: K7VIQ3
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0,02M of each monossacharide (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine), 0.1M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 9, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→39.87 Å / Num. obs: 14190 / % possible obs: 97 % / Redundancy: 4 % / Biso Wilson estimate: 55.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.027 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1492 / Num. unique obs: 1492 / CC1/2: 0.905 / Rpim(I) all: 0.341 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSMay 1, 2016 BUILT=20160617data reduction
Aimless0.5.31data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L68

4l68


Resolution: 2.3→39.87 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.296 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.211 652 4.6 %RANDOM
Rwork0.182 ---
obs0.184 14160 96.3 %-
Displacement parametersBiso mean: 66.92 Å2
Baniso -1Baniso -2Baniso -3
1-24.0965 Å20 Å20 Å2
2---12.7082 Å20 Å2
3----11.3883 Å2
Refinement stepCycle: 1 / Resolution: 2.3→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 32 65 2277
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012258HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.063076HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d753SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes336HARMONIC5
X-RAY DIFFRACTIONt_it2258HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion17.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion303SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2577SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.48 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2411 130 4.51 %
Rwork0.204 2755 -
all0.2056 2885 -
obs--96.71 %
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)
14.3148-0.3412-1.99876.0773.14086.34130.11940.1548-0.70990.14390.0213-0.49480.7060.1824-0.1407-0.23310.0657-0.0452-0.2656-0.0422-0.025416.925127.104144.9567
21.29212.9932-1.72254.9123-0.37390.03550.0364-0.0759-0.40160.0056-0.24710.54930.2011-0.18010.2108-0.24-0.086-0.021-0.0427-0.07560.03860.758931.577443.4059
31.4910.24240.15553.07350.29971.44710.1319-0.0281-0.45980.2276-0.0728-0.25470.34420.1477-0.0592-0.24610.0433-0.0135-0.1582-0.0102-0.128417.982637.584547.3062
42.46360.6044-0.27212.7957-0.26491.40210.1864-0.22140.06810.2181-0.2020.22080.0202-0.05220.0156-0.2968-0.00740.0492-0.1078-0.0681-0.17279.874648.216647.6202
54.58910.83242.34354.7121-0.97624.77570.1351-0.63910.44990.9111-0.16550.1635-0.4522-0.22680.0304-0.0898-0.06660.0971-0.1023-0.2052-0.136516.445763.097457.7091
64.8735-0.0519-0.51342.86611.69910.023-0.02220.06760.4852-0.0343-0.2120.4802-0.0551-0.13170.2342-0.24490.03520.0135-0.1102-0.0622-0.0049.932461.358742.3465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|744 - 791}
2X-RAY DIFFRACTION2{A|792 - 810}
3X-RAY DIFFRACTION3{A|811 - 860}
4X-RAY DIFFRACTION4{A|861 - 962}
5X-RAY DIFFRACTION5{A|963 - 1023}
6X-RAY DIFFRACTION6{A|1024 - 1045}

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