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- PDB-7fgq: Crystal structure of Thymidylate kinase with TMP and its low-reso... -

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Basic information

Entry
Database: PDB / ID: 7fgq
TitleCrystal structure of Thymidylate kinase with TMP and its low-resolution (SAXS) solution structure from Brugia malayi
ComponentsdTMP kinase
KeywordsTRANSFERASE / Thymidylate Kinase / Nucleotide biosynthesis / ATP binding / Nucleotide binding / Complexed with dTMP
Function / homology
Function and homology information


dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / nucleoside diphosphate kinase activity / mitochondrion / ATP binding / nucleus / cytosol
Similarity search - Function
Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
THYMIDINE-5'-PHOSPHATE / dTMP kinase
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsRamachandran, R. / Vishwakarma, J. / Sharma, V.K.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: Crystal structure of Thymidylate kinase with TMP and its low-resolution (SAXS) solution structure from Brugia malayi
Authors: Ramachandran, R. / Vishwakarma, J. / Sharma, V.K.
History
DepositionJul 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 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

Downloads & links

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Assembly

Deposited unit
A: dTMP kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7352
Polymers28,4131
Non-polymers3221
Water1,26170
1
A: dTMP kinase
hetero molecules

A: dTMP kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4694
Polymers56,8252
Non-polymers6442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area3140 Å2
ΔGint-16 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.670, 58.670, 119.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein dTMP kinase / Thymidylate Kinase


Mass: 28412.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: Bm5401, Bm1_23075, BM_Bm5401 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P6BP23, dTMP kinase
#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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: 1.81 Å3/Da / Density % sol: 32.09 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Diammonium tartrate, Bis-Tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9784 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.91→41.881 Å / Num. obs: 16977 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Χ2: 0.94 / Net I/av σ(I): 16.2 / Net I/σ(I): 2.2
Reflection shellResolution: 1.91→8.96 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.107 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 16977 / CC1/2: 0.741 / Rpim(I) all: 0.504 / Χ2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimless7.0.072data scaling
PDB_EXTRACT3.27data extraction
iMOSFLM7.0.072data reduction
PHENIX2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1e9c

1e9c


Resolution: 1.91→41.881 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 798 4.72 %
Rwork0.2196 --
obs0.221 16913 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→41.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 21 70 1597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081551
X-RAY DIFFRACTIONf_angle_d1.082088
X-RAY DIFFRACTIONf_dihedral_angle_d10.893937
X-RAY DIFFRACTIONf_chiral_restr0.072234
X-RAY DIFFRACTIONf_plane_restr0.006262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9101-2.02980.26161360.23382613X-RAY DIFFRACTION100
2.0298-2.18650.23351340.23132637X-RAY DIFFRACTION100
2.1865-2.40650.29431210.23092625X-RAY DIFFRACTION100
2.4065-2.75470.28311520.23552655X-RAY DIFFRACTION100
2.7547-3.47040.26171140.23042729X-RAY DIFFRACTION100
3.4704-41.80.22151410.20212856X-RAY DIFFRACTION100

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