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- PDB-1e2f: Human thymidylate kinase complexed with thymidine monophosphate, ... -

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Basic information

Entry
Database: PDB / ID: 1e2f
TitleHuman thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate and a magnesium-ion
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / TREANSFERASE / 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 / 1.6 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)25,3576
Polyers24,0531
Non-polymers1,3045
Water5,350297
1
A: THYMIDYLATE KINASE
hetero molecules

A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,71312
Polyers48,1052
Non-polymers2,60810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area (Å2)6080
ΔGint (kcal/M)-71.0
Surface area (Å2)16920
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)101.300, 101.300, 49.300
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, 302 molecules

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


Mass: 322.208 Da / Num. of mol.: 1 / Formula: C10H15N2O8P
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Formula: C10H17N6O12P3 / Comment: AMP-PNP (energy-carrying molecule analogue) *YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#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.: 297 / Formula: H2O / Water

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Details

Compound detailsCHAIN A ENGINEERED MUTATION ARG200ALA GLY, SER, HIS INSERTED AT THE N-TERMINUS THE ACTIVE SITE ...CHAIN A ENGINEERED MUTATION ARG200ALA GLY, SER, HIS INSERTED AT THE N-TERMINUS THE ACTIVE SITE CONTAINS A MIXTURE OF NUCLEOTIDES: TMP ADP AND TMP + ANP, THE ORIENTATION OF TMP DIFFERS.
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: 2.63 / Density percent sol: 53.22 %
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.
Crystal grow
*PLUS
Temp: 20 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
11 mMTMP1drop
220 mMAppNHp1drop
328 mg/mlTMPK1drop
450 mM1dropMgCl2
5200 mM1dropKCl
650 mMTris-HCl1drop
715-22 %(w/v)PEG33501reservoir
85 %(v/v)dead sea water1reservoir
9100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: EMBL/DESY, HAMBURG BEAMLINE BW7B / Synchrotron site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.847
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: YES / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.847 Å / Relative weight: 1
ReflectionD resolution high: 1.6 Å / D resolution low: 71.7 Å / Number obs: 33305 / Rsym value: 0.046 / NetI over sigmaI: 20.9 / Redundancy: 3.1 % / Percent possible obs: 96.6
Reflection shellHighest resolution: 1.6 Å / Lowest resolution: 1.7 Å / MeanI over sigI obs: 4.4 / Rsym value: 0.155 / Redundancy: 3.1 % / Percent possible all: 98
Reflection
*PLUS
Number measured all: 103211 / Rmerge I obs: 0.046
Reflection shell
*PLUS
Percent possible obs: 98 / Rmerge I obs: 0.155

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0
Least-squares processR factor R free: 0.264 / R factor R work: 0.21 / Highest resolution: 1.6 Å / Lowest resolution: 71.7 Å / Number reflection R free: 3365 / Number reflection obs: 33305 / Percent reflection R free: 1 / Percent reflection obs: 96.6
Refine hist #LASTHighest resolution: 1.6 Å / Lowest resolution: 71.7 Å
Number of atoms included #LASTProtein: 1642 / Nucleic acid: 0 / Ligand: 81 / Solvent: 297 / Total: 2020
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d1.7
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
Software
*PLUS
Name: REFMAC / Classification: refinement
Least-squares process
*PLUS
R factor R work: 0.21 / R factor obs: 0.198

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