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- PDB-7wj6: Crystal Structure of the Kinase Domain of a Class III Lanthipepti... -

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Basic information

Entry
Database: PDB / ID: 7wj6
TitleCrystal Structure of the Kinase Domain of a Class III Lanthipeptide Synthetase CurKC
ComponentsSerine/threonine protein kinase
KeywordsBIOSYNTHETIC PROTEIN / Lanthipeptide Synthetase / Class III / CurKC / Curvopeptin
Function / homology
Function and homology information


peptide modification / carbohydrate metabolic process / protein serine/threonine kinase activity / ATP binding / metal ion binding
Similarity search - Function
: / RamC, N-terminal domain / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / Six-hairpin glycosidase-like superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine protein kinase
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHuang, S. / Wang, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21922703 China
National Natural Science Foundation of China (NSFC)91953112 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Discovery of a Unique Structural Motif in Lanthipeptide Synthetases for Substrate Binding and Interdomain Interactions.
Authors: Huang, S. / Wang, Y. / Cai, C. / Xiao, X. / Liu, S. / Ma, Y. / Xie, X. / Liang, Y. / Chen, H. / Zhu, J. / Hegemann, J.D. / Yao, H. / Wei, W. / Wang, H.
History
DepositionJan 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Assembly

Deposited unit
A: Serine/threonine protein kinase
B: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5028
Polymers60,3572
Non-polymers1466
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-80 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.199, 96.199, 115.453
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 18 or (resid 19...
21(chain B and (resid 7 through 40 or (resid 41...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUSERSER(chain A and (resid 7 through 18 or (resid 19...AA7 - 187 - 18
12ASNASNASNASN(chain A and (resid 7 through 18 or (resid 19...AA1919
13LEULEULEULEU(chain A and (resid 7 through 18 or (resid 19...AA7 - 2537 - 253
14LEULEULEULEU(chain A and (resid 7 through 18 or (resid 19...AA7 - 2537 - 253
15LEULEULEULEU(chain A and (resid 7 through 18 or (resid 19...AA7 - 2537 - 253
16LEULEULEULEU(chain A and (resid 7 through 18 or (resid 19...AA7 - 2537 - 253
21LEULEUALAALA(chain B and (resid 7 through 40 or (resid 41...BB7 - 407 - 40
22ARGARGARGARG(chain B and (resid 7 through 40 or (resid 41...BB4141
23ALAALALEULEU(chain B and (resid 7 through 40 or (resid 41...BB5 - 2535 - 253
24ALAALALEULEU(chain B and (resid 7 through 40 or (resid 41...BB5 - 2535 - 253
25ALAALALEULEU(chain B and (resid 7 through 40 or (resid 41...BB5 - 2535 - 253
26ALAALALEULEU(chain B and (resid 7 through 40 or (resid 41...BB5 - 2535 - 253

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Components

#1: Protein Serine/threonine protein kinase / CurKC kinase


Mass: 30178.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria)
Strain: ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9
Gene: Tcur_3610 / Production host: Escherichia coli (E. coli) / References: UniProt: D1ABX1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 0.1 M Bis-Tris, pH 6.3, 3 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→34.94 Å / Num. obs: 24666 / % possible obs: 96.86 % / Redundancy: 19.8 % / CC1/2: 1 / Net I/σ(I): 20.44
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 2421 / CC1/2: 0.332

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MRU

1mru


Resolution: 2.55→34.94 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 1635 8.09 %
Rwork0.2109 18569 -
obs0.2147 20204 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.12 Å2 / Biso mean: 65.2807 Å2 / Biso min: 37.19 Å2
Refinement stepCycle: final / Resolution: 2.55→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 6 26 3717
Biso mean--69.02 59.81 -
Num. residues----485
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1434X-RAY DIFFRACTION8.414TORSIONAL
12B1434X-RAY DIFFRACTION8.414TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.620.38471250.31691448157393
2.63-2.710.30571290.27391475160495
2.71-2.810.37061290.28291501163096
2.81-2.920.32421320.25891524165697
2.92-3.050.28731360.26361514165098
3.05-3.210.28181410.24191567170899
3.21-3.410.30851410.25041544168599
3.41-3.680.28941400.203215611701100
3.68-4.050.23691400.210815881728100
4.05-4.630.21271360.175515881724100
4.63-5.830.25821420.200916011743100
5.83-34.940.22421440.18251658180298

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