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- PDB-1e2e: Human thymidylate kinase complexed with thymidine monophosphate, ... -

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Basic information

Entry
Database: PDB / ID: 1e2e
TitleHuman thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate,a magnesium-ion and ALf3
ComponentsTHYMIDYLATE KINASE
KeywordsTHYMIDYLATE KINASE / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / 2 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 typeGroupProviderType
1.0May 17, 2001Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9356
Polyers24,0531
Non-polymers8825
Water3,099172
1
A: THYMIDYLATE KINASE
hetero molecules

A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,86912
Polyers48,1052
Non-polymers1,76410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)101.600, 101.600, 49.900
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, 177 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Formula: AlF3 / Aluminium fluoride
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Formula: H2O / Water

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Details

Compound detailsCHAIN A ENGINEERED MUTATION ARG200ALA GLY, SER, HIS INSERTED AT THE N-TERMINUS
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: 2.68 / Density percent sol: 54.05 %
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
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID14-3 / Synchrotron site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: YES / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 / Relative weight: 1
ReflectionD resolution high: 2 / D resolution low: 71.8 / Number obs: 17782 / Rsym value: 0.079 / NetI over sigmaI: 11.7 / Redundancy: 5.2 % / Percent possible obs: 99
Reflection shellHighest resolution: 2 / Lowest resolution: 2.1 / MeanI over sigI obs: 3 / Rsym value: 0.329 / Redundancy: 4.6 % / Percent possible all: 98.7

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Details: GLU 152 MODELED AS ALA DUE TO WEAK SIDE-CHAIN ELECTRON DENSITY
R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0
Least-squares processR factor R free: 0.272 / R factor R work: 0.214 / Highest resolution: 2 / Lowest resolution: 71.8 / Number reflection R free: 930 / Number reflection obs: 17782 / Percent reflection R free: 5.2 / Percent reflection obs: 99
Refine hist #LASTHighest resolution: 2 / Lowest resolution: 71.8
Number of atoms included #LASTProtein: 1616 / Nucleic acid: 0 / Ligand: 54 / Solvent: 172 / Total: 1842
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d1.6
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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