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- PDB-5yzv: Biophysical and structural characterization of the thermostable W... -

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Basic information

Entry
Database: PDB / ID: 5yzv
TitleBiophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA
ComponentsProbable serine/threonine-protein kinase PkwA
KeywordsPROTEIN BINDING / prokaryotic / thermostable / reversible folding
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeat ...G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40 repeat / WD40-repeat-containing domain superfamily / Protein kinase domain / WD40/YVTN repeat-like-containing domain superfamily / 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
Probable serine/threonine-protein kinase PkwA
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, D.Y. / Shen, C. / Du, Y. / Qiao, F.F. / Kong, T. / Yuan, L.R. / Zhang, D.L. / Wu, X.H. / Wu, Y.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21133002 China
CitationJournal: Sci Rep / Year: 2018
Title: Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA
Authors: Shen, C. / Du, Y. / Qiao, F. / Kong, T. / Yuan, L. / Zhang, D. / Wu, X. / Li, D. / Wu, Y.D.
History
DepositionDec 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable serine/threonine-protein kinase PkwA
B: Probable serine/threonine-protein kinase PkwA
C: Probable serine/threonine-protein kinase PkwA
D: Probable serine/threonine-protein kinase PkwA
E: Probable serine/threonine-protein kinase PkwA


Theoretical massNumber of molelcules
Total (without water)159,9845
Polymers159,9845
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, possible pentamer formed by association of PkwA molecules
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.687, 107.257, 110.267
Angle α, β, γ (deg.)78.77, 89.33, 88.91
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPROPROAA451 - 73811 - 298
21ASNASNPROPROBB451 - 73811 - 298
12GLUGLUPROPROAA449 - 7389 - 298
22GLUGLUPROPROCC449 - 7389 - 298
13GLUGLUPROPROAA449 - 7389 - 298
23GLUGLUPROPRODD449 - 7389 - 298
14GLUGLUPROPROAA452 - 73812 - 298
24GLUGLUPROPROEE452 - 73812 - 298
15ASNASNTRPTRPBB451 - 73711 - 297
25ASNASNTRPTRPCC451 - 73711 - 297
16ASNASNPROPROBB451 - 73811 - 298
26ASNASNPROPRODD451 - 73811 - 298
17ASNASNPROPROBB451 - 73811 - 298
27ASNASNPROPROEE451 - 73811 - 298
18GLUGLUPROPROCC449 - 7389 - 298
28GLUGLUPROPRODD449 - 7389 - 298
19GLUGLUPROPROCC452 - 73812 - 298
29GLUGLUPROPROEE452 - 73812 - 298
110GLUGLUPROPRODD452 - 73812 - 298
210GLUGLUPROPROEE452 - 73812 - 298

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.130477, 0.180498, -0.974883), (0.085575, -0.977569, -0.192448), (-0.987751, -0.108535, 0.112104)9.12894, 22.8981, 17.43775

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Components

#1: Protein
Probable serine/threonine-protein kinase PkwA


Mass: 31996.855 Da / Num. of mol.: 5 / Fragment: UNP residues 441-742
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Gene: pkwA, pkw1 / Plasmid: pET-28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P49695, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, and 2.0 M Ammonium sulfate with additive from Hampton Research Silver Bullet additive Kit.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 62971 / % possible obs: 93.2 % / Redundancy: 2.9 % / Net I/σ(I): 11.33
Reflection shellResolution: 2.5→2.54 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50.01 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.882 / SU B: 24.147 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.716 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25912 2665 4.9 %RANDOM
Rwork0.22474 ---
obs0.22645 51766 90.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20.6 Å2-0.15 Å2
2---0.56 Å2-1.36 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 2.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10697 0 0 230 10927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.01910951
X-RAY DIFFRACTIONr_bond_other_d0.0120.029806
X-RAY DIFFRACTIONr_angle_refined_deg2.1261.91814992
X-RAY DIFFRACTIONr_angle_other_deg3.319322536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12251429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15123.688480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.344151491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3291562
X-RAY DIFFRACTIONr_chiral_restr0.1250.21697
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112720
X-RAY DIFFRACTIONr_gen_planes_other0.0130.022522
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_it3.4852.5485737
X-RAY DIFFRACTIONr_mcbond_other3.4842.5485736
X-RAY DIFFRACTIONr_mcangle_it5.4223.8147159
X-RAY DIFFRACTIONr_mcangle_other5.4223.8147160
X-RAY DIFFRACTIONr_scbond_it5.9063.2365214
X-RAY DIFFRACTIONr_scbond_other5.9063.2355214
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9944.637833
X-RAY DIFFRACTIONr_long_range_B_refined12.52623.40512434
X-RAY DIFFRACTIONr_long_range_B_other12.52223.3412395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1010A2338tight positional1.170.1
11A2349tight thermal8.331
22A2336tight thermal8.661
33A2348tight thermal4.691
44A2341tight thermal7.281
55B2370tight thermal7.491
66B2346tight thermal7.651
77B2413tight thermal5.591
88C2334tight thermal7.911
99C2371tight thermal7.611
1010D2338tight thermal6.621
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 136 -
Rwork0.28 3036 -
obs--71.52 %
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)
10.67450.06860.04710.8169-0.29380.78230.04850.08220.04610.05150.02480.0513-0.0701-0.0406-0.07330.0172-0.00250.01070.16950.13270.124429.7159-0.1006-4.0968
21.58270.3659-0.41990.9406-0.40340.91330.03920.0135-0.03490.0628-0.01880.0147-0.06610.0459-0.02040.00880.00610.0150.09860.11210.14216.66728.3303-18.3634
31.3194-0.03670.37150.7156-0.43691.39330.02330.05450.0093-0.01260.0114-0.02380.04440.0128-0.03470.0179-0.0010.01780.19990.11520.095123.091954.5099-48.7304
41.3189-0.07250.51510.6550.11171.79620.0342-0.10230.081-0.0340.0025-0.01710.0871-0.0482-0.03670.0263-0.00750.01610.19420.09440.080336.328562.6746-79.4668
50.6012-0.03390.43851.26690.55051.0108-0.02240.12050.00260.14080.0729-0.10110.12830.085-0.05050.0406-0.00870.00270.15010.04870.068942.448771.2107-12.0524
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A448 - 738
2X-RAY DIFFRACTION2B451 - 738
3X-RAY DIFFRACTION3C449 - 738
4X-RAY DIFFRACTION4D449 - 738
5X-RAY DIFFRACTION5E451 - 738

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