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- PDB-1mrn: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINAS... -

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Basic information

Entry
Database: PDB / ID: 1mrn
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH BISUBSTRATE INHIBITOR (TP5A)
ComponentsThymidylate Kinase
KeywordsTRANSFERASE / TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE) / KINASE
Function / homology
Function and homology information


TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding ...TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHaouz, A. / Vanheusden, V. / Munier-Lehmann, H. / Froeyen, M. / Herdewijn, P. / Van Calenbergh, S. / Delarue, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism.
Authors: Haouz, A. / Vanheusden, V. / Munier-Lehmann, H. / Froeyen, M. / Herdewijn, P. / Van Calenbergh, S. / Delarue, M.
History
DepositionSep 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidylate Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7705
Polymers22,6631
Non-polymers1,1084
Water1,04558
1
A: Thymidylate Kinase
hetero molecules

A: Thymidylate Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,54110
Polymers45,3252
Non-polymers2,2168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)75.460, 75.460, 133.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe molecule is normally a dimer in solution. The other monomer (B) can be generated by applying the transformation X, -Y, -Z to molecule A.

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Components

#1: Protein Thymidylate Kinase / dTMP kinase / Thymidylic kinase / TMPK


Mass: 22662.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET22B / Production host: Escherichia coli (E. coli)
References: UniProt: O05891, UniProt: P9WKE1*PLUS, dTMP kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-T5A / P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE


Mass: 891.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N7O23P5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Ammonium sulfate, PEG600, MES, Magnesium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.5 mg/mlprotein1drop
25 mManalogue 11drop
334 %(w/v)ammonium sulfate1reservoir
4100 mMHEPES1reservoirpH6.0
52 %(w/v)PEG20001reservoir
620 mMmagnesium acetate1reservoir
70.5 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 30, 2002 / Details: Osmic Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 8407 / Num. obs: 8407 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.2
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 9.2 / Rsym value: 0.366 / % possible all: 90.1
Reflection
*PLUS
% possible obs: 95.1 %
Reflection shell
*PLUS
% possible obs: 90.1 % / Num. unique obs: 768

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G3U

1g3u


Resolution: 2.45→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 379 5 %RANDOM
Rwork0.236 ---
all0.239 8139 --
obs0.239 8139 92.6 %-
Solvent computationBsol: 42.56 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 38.0822 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 66 58 1666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007885
X-RAY DIFFRACTIONc_angle_deg1.20634
X-RAY DIFFRACTIONc_dihedral_angle_d20.08821
X-RAY DIFFRACTIONc_improper_angle_d0.76103
LS refinement shellResolution: 2.45→2.54 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2864 23 5 %
Rwork0.3076 688 -
obs-688 -
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0079
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76103

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