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- PDB-2ja1: Thymidine kinase from B. cereus with TTP bound as phosphate donor. -

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Basic information

Entry
Database: PDB / ID: 2ja1
TitleThymidine kinase from B. cereus with TTP bound as phosphate donor.
ComponentsTHYMIDINE KINASE
KeywordsTRANSFERASE / TK1 / DNK / LASSO / KINASE / PHOSPHATE DONOR / DEOXYRIBONUCLEOSIDE KINASE
Function / homology
Function and homology information


thymidine kinase / thymidine kinase activity / DNA biosynthetic process / zinc ion binding / ATP binding / cytoplasm
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / Thymidine kinase / :
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 17, 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 1.2Sep 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rrim_I_all ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rrim_I_all / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5334
Polymers21,8671
Non-polymers6663
Water36020
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)90,13116
Polymers87,4684
Non-polymers2,66312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)95.390, 95.390, 204.862
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: 21866.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: DVI / Variant: 98-7869 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KY895
References: UniProt: Q0H9H6, UniProt: Q0H0H6*PLUS, 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-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 5.3 Å3/Da / Density % sol: 76.6 %
Crystal growpH: 7 / Details: 60% MPD 0.1M HEPES PH7, pH 7.00

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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: 2.8→37.6 Å / Num. obs: 12035 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Rrim(I) all: 0.1 / Net I/σ(I): 26.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 14 % / Mean I/σ(I) obs: 4.2 / Rrim(I) all: 0.534 / % 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: PDB ENTRY 2J9R

2j9r


Resolution: 2.8→37.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 17.574 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 574 4.8 %RANDOM
Rwork0.196 ---
obs0.198 11450 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å20 Å20 Å2
2--3.34 Å20 Å2
3----6.68 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 38 20 1557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221567
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9772130
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95923.97373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67515258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6961512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021179
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.2649
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21046
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4761.5976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87221557
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.333645
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2434.5573
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: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.394 53
Rwork0.352 795
Refinement TLS params.Method: refined / Origin x: 12.0244 Å / Origin y: 8.8685 Å / Origin z: 12.6826 Å
111213212223313233
T-0.138 Å20.0397 Å2-0.0243 Å2--0.0656 Å2-0.0526 Å2---0.1998 Å2
L2.9811 °2-1.0101 °2-0.2014 °2-4.9808 °2-0.0342 °2--3.2741 °2
S0.0813 Å °-0.348 Å °0.156 Å °0.3534 Å °0.0032 Å °-0.4679 Å °-0.3036 Å °0.6285 Å °-0.0845 Å °

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