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- PDB-8yks: PaThiL in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 8yks
TitlePaThiL in complex with AMP-PNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Thiamine-monophosphate kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
SupersessionMar 12, 2025ID: 7DU3
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Thiamine-monophosphate kinase
A: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,58917
Polymers70,9912
Non-polymers1,59915
Water8,197455
1
B: Thiamine-monophosphate kinase
hetero molecules

B: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,42516
Polymers70,9912
Non-polymers1,43414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9280 Å2
ΔGint-136 kcal/mol
Surface area25250 Å2
MethodPISA
2
A: Thiamine-monophosphate kinase
hetero molecules

A: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,75418
Polymers70,9912
Non-polymers1,76316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7450 Å2
ΔGint-124 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.190, 115.460, 132.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-667-

HOH

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Components

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Protein , 1 types, 2 molecules BA

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


Mass: 35495.383 Da / Num. of mol.: 2
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 , 7 types, 470 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 0.061 M Tris HCl, 0.039 M Bicine, pH 8.5, 20% v/v PEG 500 MME, ...Details: 0.02 M DL-glutamic acid monohydrate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine monohydrochloride, 0.02 M DL-serine, 0.061 M Tris HCl, 0.039 M Bicine, pH 8.5, 20% v/v PEG 500 MME, 10% w/v PEG 20000 (Morpheus H9)

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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: 1.8→50 Å / Num. obs: 80499 / % possible obs: 99.97 % / Redundancy: 13.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09512 / Net I/σ(I): 19.04
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 1.022 / Num. unique obs: 7959 / CC1/2: 0.823

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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: 1.8→43.54 Å / SU ML: 0.208 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9817
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1979 7792 5 %
Rwork0.1822 147965 -
obs0.183 80410 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.78 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4595 0 95 455 5145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834766
X-RAY DIFFRACTIONf_angle_d1.06856500
X-RAY DIFFRACTIONf_chiral_restr0.0618752
X-RAY DIFFRACTIONf_plane_restr0.0062854
X-RAY DIFFRACTIONf_dihedral_angle_d19.94421682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.42462580.39244840X-RAY DIFFRACTION98.74
1.82-1.840.29082570.30224962X-RAY DIFFRACTION99.96
1.84-1.860.31732600.27034908X-RAY DIFFRACTION100
1.86-1.890.25972610.24374927X-RAY DIFFRACTION99.98
1.89-1.910.28192630.23184952X-RAY DIFFRACTION100
1.91-1.940.24562580.22494934X-RAY DIFFRACTION100
1.94-1.970.21912660.20894949X-RAY DIFFRACTION99.98
1.97-1.990.22052610.20884895X-RAY DIFFRACTION99.98
1.99-2.030.2372600.20394981X-RAY DIFFRACTION100
2.03-2.060.20692540.19554866X-RAY DIFFRACTION100
2.06-2.090.23652630.19924998X-RAY DIFFRACTION100
2.09-2.130.25142610.18944934X-RAY DIFFRACTION100
2.13-2.170.21372560.18764917X-RAY DIFFRACTION100
2.17-2.220.21022580.19114926X-RAY DIFFRACTION100
2.22-2.270.22432570.18584932X-RAY DIFFRACTION100
2.27-2.320.21222630.19064977X-RAY DIFFRACTION99.98
2.32-2.380.18942600.18414927X-RAY DIFFRACTION100
2.38-2.440.19242540.18924923X-RAY DIFFRACTION99.98
2.44-2.510.19342620.18494968X-RAY DIFFRACTION100
2.51-2.590.19672560.18834893X-RAY DIFFRACTION100
2.59-2.690.21462630.1814976X-RAY DIFFRACTION100
2.69-2.790.2352550.18564929X-RAY DIFFRACTION100
2.79-2.920.21192620.18094906X-RAY DIFFRACTION100
2.92-3.080.16912610.184940X-RAY DIFFRACTION100
3.08-3.270.22382600.17684932X-RAY DIFFRACTION99.98
3.27-3.520.20562540.17224956X-RAY DIFFRACTION100
3.52-3.870.1632590.15734942X-RAY DIFFRACTION100
3.88-4.440.14592640.15284924X-RAY DIFFRACTION99.87
4.44-5.590.16982600.15674916X-RAY DIFFRACTION99.98
5.59-43.540.17072660.17934935X-RAY DIFFRACTION99.79

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