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- PDB-9dk2: Lexapeptide dehydratase complex LxmKY, ATP bound -

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Basic information

Entry
Database: PDB / ID: 9dk2
TitleLexapeptide dehydratase complex LxmKY, ATP bound
Components
  • Kinase
  • Lyase
KeywordsBIOSYNTHETIC PROTEIN / Kinase / Lyase / lanthipeptide dehydratase / complex
Function / homology
Function and homology information


HopA1 effector protein / HopA1 effector protein family / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETIC ACID / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Aminoglycoside phosphotransferase domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesStreptomyces rochei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)83,3628
Polymers82,5592
Non-polymers8036
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-36 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.716, 120.661, 152.767
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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 , 6 types, 77 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M Bis-Tris propane 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: Mar 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→49.282 Å / Num. obs: 37827 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.089 / Rrim(I) all: 0.239 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.1 % / Rmerge(I) obs: 4.278 / Num. unique obs: 4216 / CC1/2: 0.623 / Rpim(I) all: 1.735 / Rrim(I) all: 4.619 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
Aimless1.12.13data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.282 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: FREE R-VALUE / ESU R: 0.312 / ESU R Free: 0.251
RfactorNum. reflection% reflection
Rfree0.2676 1916 5.074 %
Rwork0.2243 35847 -
all0.227 --
obs-37783 99.947 %
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: 70.592 Å2
Baniso -1Baniso -2Baniso -3
1--3.765 Å2-0 Å20 Å2
2--4.385 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 48 71 4876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124920
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164447
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.6396720
X-RAY DIFFRACTIONr_angle_other_deg0.8131.54910275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0925641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.7821054
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42210662
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.93210200
X-RAY DIFFRACTIONr_chiral_restr0.060.2766
X-RAY DIFFRACTIONr_chiral_restr_other1.5370.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025815
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02986
X-RAY DIFFRACTIONr_nbd_refined0.2280.21053
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2310.24018
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22373
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1140.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.22
X-RAY DIFFRACTIONr_nbd_other0.2570.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0850.21
X-RAY DIFFRACTIONr_mcbond_it6.277.4662586
X-RAY DIFFRACTIONr_mcbond_other6.2617.4662585
X-RAY DIFFRACTIONr_mcangle_it9.23811.1783219
X-RAY DIFFRACTIONr_mcangle_other9.23711.1783220
X-RAY DIFFRACTIONr_scbond_it6.2267.7172334
X-RAY DIFFRACTIONr_scbond_other6.2247.7162335
X-RAY DIFFRACTIONr_scangle_it9.11511.423501
X-RAY DIFFRACTIONr_scangle_other9.11411.4213502
X-RAY DIFFRACTIONr_lrange_it12.07990.8875240
X-RAY DIFFRACTIONr_lrange_other12.08190.8945239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.3821440.392606X-RAY DIFFRACTION99.9273
2.565-2.6350.3331330.3422554X-RAY DIFFRACTION99.8143
2.635-2.7110.3411340.3042424X-RAY DIFFRACTION99.9219
2.711-2.7940.3371290.2922396X-RAY DIFFRACTION100
2.794-2.8860.3471290.2812355X-RAY DIFFRACTION99.9598
2.886-2.9860.3131130.2582246X-RAY DIFFRACTION100
2.986-3.0990.263980.2472218X-RAY DIFFRACTION100
3.099-3.2250.3121340.2512083X-RAY DIFFRACTION99.9549
3.225-3.3670.3211090.2322007X-RAY DIFFRACTION99.9528
3.367-3.5310.2871020.2411939X-RAY DIFFRACTION100
3.531-3.7210.225920.2131855X-RAY DIFFRACTION100
3.721-3.9450.241860.1951749X-RAY DIFFRACTION100
3.945-4.2160.222880.1941664X-RAY DIFFRACTION100
4.216-4.5510.276960.1991539X-RAY DIFFRACTION100
4.551-4.9810.221800.1831420X-RAY DIFFRACTION100
4.981-5.5620.269610.2121324X-RAY DIFFRACTION100
5.562-6.4090.302620.2251178X-RAY DIFFRACTION100
6.409-7.8160.243570.206989X-RAY DIFFRACTION100
7.816-10.9170.17410.161801X-RAY DIFFRACTION100

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