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- PDB-2j9r: Thymidine kinase from B. anthracis in complex with dT. -

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Basic information

Entry
Database: PDB / ID: 2j9r
TitleThymidine kinase from B. anthracis in complex with dT.
ComponentsTHYMIDINE KINASE
KeywordsTRANSFERASE / TK1 / DNK / LASSO / KINASE / ATP-BINDING / DEOXYRIBONUCLEOSIDE KINASE / DNA SYNTHESIS / PHOSPHATE ACCEPTOR / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


thymidine metabolic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich ...Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / THYMIDINE / Thymidine kinase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKosinska, U. / Carnrot, C. / Sandrini, M.P.B. / Clausen, A.R. / Wang, L. / Piskur, J. / Eriksson, S. / Eklund, H.
CitationJournal: FEBS J. / Year: 2007
Title: Structural Studies of Thymidine Kinases from Bacillus Anthracis and Bacillus Cereus Provide Insights Into Quaternary Structure and Conformational Changes Upon Substrate Binding
Authors: Kosinska, U. / Carnrot, C. / Sandrini, M.P.B. / Clausen, A.R. / Wang, L. / Piskur, J. / Eriksson, S. / Eklund, H.
History
DepositionNov 15, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2444
Polymers23,8411
Non-polymers4033
Water34219
1
A: THYMIDINE KINASE
hetero molecules

A: THYMIDINE KINASE
hetero molecules

A: THYMIDINE KINASE
hetero molecules

A: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,97516
Polymers95,3654
Non-polymers1,61012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation15_465y-1,x+1,-z1
crystal symmetry operation10_465-x-1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.171, 73.171, 223.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein THYMIDINE KINASE


Mass: 23841.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: STERNE / Variant: 34F2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q81JX0, thymidine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O5
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growpH: 6
Details: 5% 1,2-PROPANEDIOL 0.1M NA/K PHOSPHATE PH 6 10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→25.87 Å / Num. obs: 8799 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDP ENTRY 1XMR

1xmr
PDB Unreleased entry


Resolution: 2.7→25.87 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / SU B: 16.998 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.244 415 4.7 %RANDOM
Rwork0.203 ---
obs0.205 8366 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.79 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2--2.51 Å20 Å2
3----5.02 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 23 19 1427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9661943
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09923.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52415242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8421511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021082
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2600
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2974
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4561.5908
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84121437
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1323583
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.884.5506
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.42 31
Rwork0.26 598
Refinement TLS params.Method: refined / Origin x: -34.1328 Å / Origin y: 18.4702 Å / Origin z: -1.5512 Å
111213212223313233
T0.0593 Å2-0.0006 Å20.0516 Å2--0.1821 Å20.0009 Å2---0.089 Å2
L1.979 °20.0031 °2-0.3139 °2-1.8095 °20.0878 °2--3.3625 °2
S-0.0295 Å °0.0318 Å °-0.4261 Å °-0.0859 Å °-0.0307 Å °0.045 Å °0.9255 Å °0.0935 Å °0.0602 Å °

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