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- PDB-7du3: ThiL in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 7du3
TitleThiL in complex with AMP-PNP
ComponentsThiamine-monophosphate kinase
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


thiamine-phosphate kinase / thiamine-phosphate kinase activity / thiamine diphosphate biosynthetic process / thiamine 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: 2.54 Å
AuthorsLin, J.Q. / Lescar, J.
CitationJournal: To Be Published
Title: ThiL in complex with AMP-PNP
Authors: Lin, J.Q. / Lescar, J.
History
DepositionJan 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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: Thiamine-monophosphate kinase
B: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,40512
Polymers70,9912
Non-polymers1,41510
Water2,900161
1
A: Thiamine-monophosphate kinase
hetero molecules

B: Thiamine-monophosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,40512
Polymers70,9912
Non-polymers1,41510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
Buried area3550 Å2
ΔGint-26 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.820, 115.800, 132.470
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
11B-582-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 19 through 329)
d_2ens_1(chain "B" and resid 19 through 329)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TYRLEUA1 - 311
d_21ens_1TYRLEUE8 - 318

NCS oper: (Code: givenMatrix: (0.00185795606976, -0.999395262971, 0.0347225625533), (-0.99802011519, -0.00403611155889, -0.062765910168), (0.0628680974341, -0.0345371995754, -0.997424074389)Vector: ...NCS oper: (Code: given
Matrix: (0.00185795606976, -0.999395262971, 0.0347225625533), (-0.99802011519, -0.00403611155889, -0.062765910168), (0.0628680974341, -0.0345371995754, -0.997424074389)
Vector: 57.5195926298, 58.5042596307, 30.311967835)

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Components

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Protein , 1 types, 2 molecules AB

#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 , 5 types, 171 molecules

#2: 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
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.02M DL-glutamic acid monohydrate, 0.02M DL-alanine, 0.02M glycine, 0.02M DL-lysine monohydrochloride, 0.02M DL-serine, 0.061M Tris, 0.039M Bicine, pH 8.5, 20% v/v PEG 500 MME, 10% w/v PEG 20000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→48 Å / Num. obs: 28688 / % possible obs: 99.3 % / Redundancy: 13.7 % / Biso Wilson estimate: 51.94 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.04875 / Rrim(I) all: 0.1817 / Net I/σ(I): 16.75
Reflection shellResolution: 2.543→2.634 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.367 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 2670 / CC1/2: 0.732 / CC star: 0.919 / Rpim(I) all: 0.3884 / % possible all: 93.55

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XEP

6xep


Resolution: 2.54→43.59 Å / SU ML: 0.315 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.5381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2098 2746 5.02 %
Rwork0.1713 51964 -
obs0.1733 28680 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.97 Å2
Refinement stepCycle: LAST / Resolution: 2.54→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 85 161 4833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874753
X-RAY DIFFRACTIONf_angle_d1.08756484
X-RAY DIFFRACTIONf_chiral_restr0.0564750
X-RAY DIFFRACTIONf_plane_restr0.0071853
X-RAY DIFFRACTIONf_dihedral_angle_d17.63931677
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.710477003323 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.590.3841200.31872250X-RAY DIFFRACTION84.98
2.59-2.630.28841360.25832600X-RAY DIFFRACTION100
2.63-2.680.28671390.252648X-RAY DIFFRACTION99.96
2.68-2.740.24961370.23882552X-RAY DIFFRACTION100
2.74-2.80.28831360.23832658X-RAY DIFFRACTION100
2.8-2.860.3041360.21112610X-RAY DIFFRACTION100
2.86-2.940.26621380.21812626X-RAY DIFFRACTION100
2.94-3.010.2811390.20622609X-RAY DIFFRACTION99.96
3.01-3.10.28191410.20582647X-RAY DIFFRACTION100
3.1-3.20.24241350.19032579X-RAY DIFFRACTION100
3.2-3.320.23811390.19232648X-RAY DIFFRACTION100
3.32-3.450.18261370.18322597X-RAY DIFFRACTION100
3.45-3.610.19751370.16872617X-RAY DIFFRACTION100
3.61-3.80.18631400.14562632X-RAY DIFFRACTION100
3.8-4.040.18461390.15262620X-RAY DIFFRACTION100
4.04-4.350.1921390.13922606X-RAY DIFFRACTION99.93
4.35-4.780.1631370.13272623X-RAY DIFFRACTION100
4.78-5.470.19541390.14462602X-RAY DIFFRACTION100
5.47-6.890.16261400.1842625X-RAY DIFFRACTION100
6.89-43.590.19721420.14032615X-RAY DIFFRACTION99.53

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