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- PDB-1e2g: Human thymidylate kinase complexed with ADP, TDP and a magnesium-ion -

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Basic information

Entry
Database: PDB / ID: 1e2g
TitleHuman thymidylate kinase complexed with ADP, TDP and a magnesium-ion
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / P-LOOP
Function / homologyInterconversion of nucleotide di- and triphosphates / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / P-loop containing nucleoside triphosphate hydrolase / Thymidylate kinase, conserved site / Thymidylate kinase / nucleoside monophosphate kinase activity / dUDP biosynthetic process / uridylate kinase activity ...Interconversion of nucleotide di- and triphosphates / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / P-loop containing nucleoside triphosphate hydrolase / Thymidylate kinase, conserved site / Thymidylate kinase / nucleoside monophosphate kinase activity / dUDP biosynthetic process / uridylate kinase activity / dTMP kinase / dTDP biosynthetic process / thymidylate kinase activity / myoblast differentiation / nucleoside diphosphate kinase activity / nucleobase-containing small molecule interconversion / dTTP biosynthetic process / cellular response to growth factor stimulus / mitochondrial intermembrane space / response to cadmium ion / mitochondrial matrix / response to estrogen / cell population proliferation / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm / Thymidylate kinase
Function and homology information
Specimen sourceHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.7 Å resolution
AuthorsOstermann, N. / Schlichting, I. / Brundiers, R. / Konrad, M. / Reinstein, J. / Veit, T. / Goody, R.S. / Lavie, A.
CitationJournal: Structure / Year: 2000
Title: Insights Into the Phosphoryltransfer Mechanism of Human Thymidylate Kinase Gained from Crystal Structures of Enzyme Complexes Along the Reaction Coordinate
Authors: Ostermann, N. / Schlichting, I. / Brundiers, R. / Konrad, M. / Reinstein, J. / Veit, T. / Goody, R.S. / Lavie, A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 22, 2000 / Release: May 17, 2001
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 17, 2001Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jun 28, 2017Structure modelData collectiondiffrn_source_diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2536
Polyers24,0531
Non-polymers1,2005
Water4,846269
1
A: THYMIDYLATE KINASE
hetero molecules

A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,50512
Polyers48,1052
Non-polymers2,40010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area (Å2)6240
ΔGint (kcal/M)-89.6
Surface area (Å2)16510
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)101.100, 101.100, 49.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP 43 21 2

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide THYMIDYLATE KINASE / / TMPK


Mass: 24052.533 Da / Num. of mol.: 1 / Mutation: YES / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23919, dTMP kinase

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Non-polymers , 5 types, 274 molecules

#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Formula: C10H15N2O8P
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#4: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Formula: C10H16N2O11P2 / Thymidine diphosphate
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Formula: H2O / Water

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 200 TO ALA GLY, SER, HIS INSERTED AT THE N-TERMINUS THE ACTIVE ...ENGINEERED RESIDUE IN CHAIN A, ARG 200 TO ALA GLY, SER, HIS INSERTED AT THE N-TERMINUS THE ACTIVE SITE CONTAINS A MIXTURE OF NUCLEOTIDES, ADP TMP AND ADP + TDP. CORRESPONDINGLY, THE P-LOOP HAS TWO CONFORMATIONS.
Sequence detailsSAMPLE COMTAINS SER183, ILE184, ASP190, AND A ILE191 (CONFIRMED BY THE DNA SEQUENCE AND ELECTRON ...SAMPLE COMTAINS SER183, ILE184, ASP190, AND A ILE191 (CONFIRMED BY THE DNA SEQUENCE AND ELECTRON DENSITY OF SIDE-CHAINS). POSSIBLE ERROR IN SWISSPROT ENTRY.

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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: 2.61 / Density percent sol: 52.94 %
Crystal growpH: 8
Details: VAPOR DIFFUSION AT 293 K MIXING 2 MICROLITERS OF A SOLUTION CONTAINING THE ENZYME, NUCLEOTIDES, AND 50 MM MGCL2 WITH 2 MICROLITERS OF A SOLUTION CONTAINING 21% PEG 3350, 100 MM TRIS HCL PH 8.0 AND 50 MICROLITERS OF DEAD SEA WATER.

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Details: MIRROR / Detector: IMAGE PLATE
RadiationMonochromator: NO / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionD resolution high: 1.7 Å / D resolution low: 50.5 Å / Number obs: 28445 / Rsym value: 0.052 / NetI over sigmaI: 19 / Redundancy: 4.9 % / Percent possible obs: 99.4
Reflection shellHighest resolution: 1.7 Å / Lowest resolution: 1.8 Å / MeanI over sigI obs: 3.7 / Rsym value: 0.296 / Redundancy: 4.5 % / Percent possible all: 99.6

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0
Least-squares processR factor R free: 0.24 / R factor R work: 0.191 / Highest resolution: 1.7 Å / Lowest resolution: 50.5 Å / Number reflection R free: 2859 / Number reflection obs: 28445 / Percent reflection R free: 0.1 / Percent reflection obs: 99.4
Refine hist #LASTHighest resolution: 1.7 Å / Lowest resolution: 50.5 Å
Number of atoms included #LASTProtein: 1608 / Nucleic acid: 0 / Ligand: 75 / Solvent: 269 / Total: 1952
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d1.3
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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