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- PDB-8yku: PaThiL in complex with AMP-PNP and TMP -

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Basic information

Entry
Database: PDB / ID: 8yku
TitlePaThiL in complex with AMP-PNP and TMP
ComponentsThiamine-monophosphate kinase
KeywordsPROTEIN BINDING / Complex / kinase
Function / homology
Function and homology information


thiamine-phosphate kinase / thiamine-phosphate kinase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Thiamine-monophosphate kinase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain
Similarity search - Domain/homology
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER / THIAMIN PHOSPHATE / Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsLin, J.Q. / Chung, Z. / Lescar, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: ThiL in complex with AMP-PNP
Authors: Lin, J.Q. / Lescar, J.
History
DepositionMar 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,40418
Polymers35,4951
Non-polymers1,90917
Water3,639202
1
A: Thiamine-monophosphate kinase
hetero molecules

A: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,80936
Polymers70,9912
Non-polymers3,81834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area10220 Å2
ΔGint-207 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.590, 118.590, 131.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thiamine-monophosphate kinase / Thiamine-phosphate kinase


Mass: 35495.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: thiL, CAZ10_30480, DY930_26150, FDK04_05055, IPC116_27470, IPC1323_04495, IPC1509_03965, IPC582_16370, IPC620_29520, NCTC13621_06786
Production host: Escherichia coli (E. coli) / References: UniProt: A0A232BM78, thiamine-phosphate kinase

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Non-polymers , 8 types, 219 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TPS / THIAMIN PHOSPHATE


Mass: 345.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N4O4PS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.77 Å3/Da / Density % sol: 67.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium acetate hydrate, 0.1M sodium cacodylate pH 6.5, 40% (v/v) PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953721724543 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953721724543 Å / Relative weight: 1
ReflectionResolution: 2.17→51.35 Å / Num. obs: 29549 / % possible obs: 99.98 % / Redundancy: 33.2 % / CC1/2: 0.998 / CC star: 1 / Rpim(I) all: 0.04168 / Net I/σ(I): 17.37
Reflection shellResolution: 2.17→2.248 Å / Num. unique obs: 2895 / CC1/2: 0.917 / CC star: 0.978 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Cootmodel building
MOLREPphasing
PHENIXVersion 1.18.2-3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→51.35 Å / SU ML: 0.1557 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.1932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1759 2774 5.04 %
Rwork0.1694 52230 -
obs0.1698 29548 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.4 Å2
Refinement stepCycle: LAST / Resolution: 2.17→51.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 110 202 2488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712313
X-RAY DIFFRACTIONf_angle_d0.9253142
X-RAY DIFFRACTIONf_chiral_restr0.05360
X-RAY DIFFRACTIONf_plane_restr0.0054408
X-RAY DIFFRACTIONf_dihedral_angle_d24.3403816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.210.21781380.20652601X-RAY DIFFRACTION99.49
2.21-2.250.22241410.19782614X-RAY DIFFRACTION100
2.25-2.290.19291380.19622579X-RAY DIFFRACTION100
2.29-2.340.17471400.1932618X-RAY DIFFRACTION99.93
2.34-2.390.21481330.1952614X-RAY DIFFRACTION100
2.39-2.440.16921380.18332615X-RAY DIFFRACTION100
2.44-2.50.17151460.17612607X-RAY DIFFRACTION99.96
2.5-2.570.19381400.17332628X-RAY DIFFRACTION100
2.57-2.650.23871380.17622610X-RAY DIFFRACTION100
2.65-2.730.1621440.16942599X-RAY DIFFRACTION100
2.73-2.830.20181410.17472629X-RAY DIFFRACTION100
2.83-2.940.16751350.16782597X-RAY DIFFRACTION100
2.94-3.080.20321300.16492602X-RAY DIFFRACTION100
3.08-3.240.15241380.16192626X-RAY DIFFRACTION100
3.24-3.440.18391350.16852619X-RAY DIFFRACTION100
3.44-3.710.14721430.15952622X-RAY DIFFRACTION100
3.71-4.080.13691370.15662606X-RAY DIFFRACTION100
4.08-4.670.1571380.13622613X-RAY DIFFRACTION99.96
4.67-5.880.17631400.16782612X-RAY DIFFRACTION100
5.88-51.350.19561410.18192619X-RAY DIFFRACTION99.96

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