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- PDB-7wj7: Crystal Structure of the Kinase Domain with Adenosine of a Class ... -

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Basic information

Entry
Database: PDB / ID: 7wj7
TitleCrystal Structure of the Kinase Domain with Adenosine of a Class III Lanthipeptide Synthetase CurKC
ComponentsSerine/threonine protein kinaseSerine/threonine-specific protein kinase
KeywordsBIOSYNTHETIC PROTEIN / Lanthipeptide Synthetase / Class III / CurKC / curvopeptin
Function / homology
Function and homology information


carbohydrate metabolic process / protein phosphorylation / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / Lanthionine synthetase C-like protein / 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
Chem-XYA / 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 / pdbx_initial_refinement_model

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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)60,8914
Polymers60,3572
Non-polymers5342
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-16 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.228, 96.228, 115.482
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 30178.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Adenosine
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-XYA / 2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 9-BETA-D-XYLOFURANOSYL-ADENINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 51.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Bis-Tris, pH 6.0, 3.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.55→19.82 Å / Num. obs: 20611 / % possible obs: 99.98 % / Redundancy: 19.8 % / CC1/2: 0.999 / Net I/σ(I): 20.3
Reflection shellResolution: 2.55→2.66 Å / Mean I/σ(I) obs: 5 / Num. unique obs: 2487 / CC1/2: 0.947

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Processing

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

1mru


Resolution: 2.55→19.82 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 1995 9.69 %
Rwork0.2077 18590 -
obs0.2129 20585 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.68 Å2 / Biso mean: 57.2492 Å2 / Biso min: 25.77 Å2
Refinement stepCycle: final / Resolution: 2.55→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 38 40 3847
Biso mean--81.62 51.15 -
Num. residues----488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.55-2.610.34881390.264913001439
2.61-2.680.30061430.247413271470
2.68-2.760.36071370.249612821419
2.76-2.850.29321420.239313191461
2.85-2.950.31591390.254512991438
2.95-3.070.30291430.242313301473
3.07-3.210.29861410.232113331474
3.21-3.380.29371410.226212921433
3.38-3.590.28461370.217113291466
3.59-3.860.28141410.201913401481
3.87-4.250.21561460.190813221468
4.25-4.860.23941450.171313391484
4.86-6.090.23061500.205713601510
6.09-19.820.21531510.184714181569

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