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- PDB-9dk1: Lexapeptide dehydratase complex LxmKY apo -

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Basic information

Entry
Database: PDB / ID: 9dk1
TitleLexapeptide dehydratase complex LxmKY apo
Components
  • Kinase
  • Lyase
KeywordsCYTOSOLIC PROTEIN / Kinase / lyase / complex / lanthipeptide dehydratase / BIOSYNTHETIC PROTEIN
Function / homologyHopA1 effector protein / HopA1 effector protein family / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily / ACETIC ACID / Aminoglycoside phosphotransferase domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces rochei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsRandall, G.T. / Bashiri, G.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Marsden Fund New Zealand
Other privateAuckland Medical Research Foundation
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: A Stable Dehydratase Complex Catalyzes the Formation of Dehydrated Amino Acids in a Class V Lanthipeptide.
Authors: Randall, G.T. / Grant-Mackie, E.S. / Chunkath, S. / Williams, E.T. / Middleditch, M.J. / Tao, M. / Harris, P.W.R. / Brimble, M.A. / Bashiri, G.
History
DepositionSep 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinase
B: Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8276
Polymers82,5592
Non-polymers2674
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-16 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.704, 90.280, 148.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Kinase


Mass: 43102.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal GA from proteolysed purification tag / Source: (gene. exp.) Streptomyces rochei (bacteria) / Gene: lxmK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K1TP15
#2: Protein Lyase


Mass: 39457.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal GA from proteolysed purification tag / Source: (gene. exp.) Streptomyces rochei (bacteria) / Gene: lxmY / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K1TP21

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Non-polymers , 4 types, 82 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium acetate trihydrate; 0.1 M Bis-Tris propane pH 7.5; 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.4→48.62 Å / Num. obs: 31270 / % possible obs: 100 % / Redundancy: 27.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.434 / Rpim(I) all: 0.118 / Rrim(I) all: 0.45 / Net I/σ(I): 8.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 2.794 / Num. unique obs: 3235 / CC1/2: 0.369 / Rpim(I) all: 1.433 / Rrim(I) all: 3.152 / Χ2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
Aimless0.7.8data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: FREE R-VALUE / ESU R: 0.361 / ESU R Free: 0.264
RfactorNum. reflection% reflection
Rfree0.2654 1613 5.168 %
Rwork0.2114 29598 -
all0.214 --
obs-31211 99.984 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.996 Å2
Baniso -1Baniso -2Baniso -3
1-0.368 Å20 Å20 Å2
2--1.13 Å2-0 Å2
3----1.498 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 17 78 4891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124929
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164646
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6556731
X-RAY DIFFRACTIONr_angle_other_deg0.9021.57510626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.043557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38410677
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.20710204
X-RAY DIFFRACTIONr_chiral_restr0.0630.2764
X-RAY DIFFRACTIONr_chiral_restr_other1.5370.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026060
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021136
X-RAY DIFFRACTIONr_nbd_refined0.2120.21068
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2360.24366
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22427
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2128
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0240.23
X-RAY DIFFRACTIONr_metal_ion_refined0.130.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2550.28
X-RAY DIFFRACTIONr_nbd_other0.2010.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4570.27
X-RAY DIFFRACTIONr_mcbond_it5.0725.2112599
X-RAY DIFFRACTIONr_mcbond_other5.0585.212598
X-RAY DIFFRACTIONr_mcangle_it7.299.3513234
X-RAY DIFFRACTIONr_mcangle_other7.2899.3513235
X-RAY DIFFRACTIONr_scbond_it5.8425.5072330
X-RAY DIFFRACTIONr_scbond_other5.845.5072331
X-RAY DIFFRACTIONr_scangle_it8.2829.9253496
X-RAY DIFFRACTIONr_scangle_other8.2819.9263497
X-RAY DIFFRACTIONr_lrange_it10.24248.5615294
X-RAY DIFFRACTIONr_lrange_other10.23848.5735290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3461280.3092112X-RAY DIFFRACTION99.9554
2.462-2.5290.3651060.2912122X-RAY DIFFRACTION100
2.529-2.6030.3361170.2712024X-RAY DIFFRACTION100
2.603-2.6820.335950.2571995X-RAY DIFFRACTION100
2.682-2.770.2891090.241921X-RAY DIFFRACTION100
2.77-2.8670.321940.2381884X-RAY DIFFRACTION100
2.867-2.9750.28880.2191801X-RAY DIFFRACTION100
2.975-3.0960.346850.2141743X-RAY DIFFRACTION100
3.096-3.2330.3900.2091684X-RAY DIFFRACTION100
3.233-3.390.2621090.191575X-RAY DIFFRACTION100
3.39-3.5720.216980.1911517X-RAY DIFFRACTION100
3.572-3.7880.237690.1741452X-RAY DIFFRACTION100
3.788-4.0480.218690.1751349X-RAY DIFFRACTION100
4.048-4.3690.269740.1851288X-RAY DIFFRACTION100
4.369-4.7830.224700.171177X-RAY DIFFRACTION100
4.783-5.3410.236620.21088X-RAY DIFFRACTION100
5.341-6.1550.307530.25950X-RAY DIFFRACTION100
6.155-7.5080.232430.244834X-RAY DIFFRACTION100
7.508-10.4930.2330.18665X-RAY DIFFRACTION100

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