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- PDB-1p75: Crystal structure of EHV4-TK complexed with TP5A -

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Basic information

Entry
Database: PDB / ID: 1p75
TitleCrystal structure of EHV4-TK complexed with TP5A
ComponentsThymidine kinase
KeywordsTRANSFERASE / P-loop / Lid
Function / homology
Function and homology information


TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Herpesvirus thymidine kinase / Thymidine kinase from herpesvirus / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE / Thymidine kinase
Similarity search - Component
Biological speciesEquid herpesvirus 4 (Equine herpesvirus 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsGardberg, A. / Shuvalova, L. / Monnerjahn, C. / Konrad, M. / Lavie, A.
CitationJournal: Structure / Year: 2003
Title: Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases.
Authors: Gardberg, A. / Shuvalova, L. / Monnerjahn, C. / Konrad, M. / Lavie, A.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ref_seq_dif.details / _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: Thymidine kinase
B: Thymidine kinase
C: Thymidine kinase
D: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,15624
Polymers148,0534
Non-polymers5,10220
Water2,792155
1
A: Thymidine kinase
B: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,96216
Polymers74,0272
Non-polymers2,93514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-212 kcal/mol
Surface area26290 Å2
MethodPISA
2
C: Thymidine kinase
D: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1948
Polymers74,0272
Non-polymers2,1676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-105 kcal/mol
Surface area25660 Å2
MethodPISA
3
A: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules

D: Thymidine kinase
hetero molecules

D: Thymidine kinase
hetero molecules

B: Thymidine kinase
C: Thymidine kinase
hetero molecules

B: Thymidine kinase
C: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,31148
Polymers296,1068
Non-polymers10,20540
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation3_556-x+1/2,y+1/2,-z+11
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
crystal symmetry operation3_557-x+1/2,y+1/2,-z+21
crystal symmetry operation4_457x-1/2,-y+1/2,-z+21
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area28120 Å2
ΔGint-526 kcal/mol
Surface area107550 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17530 Å2
ΔGint-335 kcal/mol
Surface area50310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.874, 117.227, 125.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D
331A
341B
351C
361D
12A
22B
32C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILESERSER3AA25 - 397 - 21
211ILEILESERSER3BB25 - 397 - 21
311ILEILESERSER3CC25 - 397 - 21
411ILEILESERSER3DD25 - 397 - 21
521PROPROVALVAL3AA59 - 7341 - 55
621PROPROVALVAL3BB59 - 7341 - 55
721PROPROVALVAL3CC59 - 7341 - 55
821PROPROVALVAL3DD59 - 7341 - 55
931GLNGLNTHRTHR3AA102 - 11684 - 98
1031GLNGLNTHRTHR3BB102 - 11684 - 98
1131GLNGLNTHRTHR3CC102 - 11684 - 98
1231GLNGLNTHRTHR3DD102 - 11684 - 98
1341VALVALSERSER3AA136 - 159118 - 141
1441VALVALSERSER3BB136 - 159118 - 141
1541VALVALSERSER3CC136 - 159118 - 141
1641VALVALSERSER3DD136 - 159118 - 141
1751ASNASNASNASN3AA178 - 185160 - 167
1851ASNASNASNASN3BB178 - 185160 - 167
1951ASNASNASNASN3CC178 - 185160 - 167
2051ASNASNASNASN3DD178 - 185160 - 167
2161ILEILEMETMET3AA208 - 217190 - 199
2261ILEILEMETMET3BB208 - 217190 - 199
2361ILEILEMETMET3CC208 - 217190 - 199
2461ILEILEMETMET3DD208 - 217190 - 199
2571LEULEULEULEU3AA267 - 276249 - 258
2671LEULEULEULEU3BB267 - 276249 - 258
2771LEULEULEULEU3CC267 - 276249 - 258
2871LEULEULEULEU3DD267 - 276249 - 258
2981ILEILETRPTRP3AA283 - 289265 - 271
3081ILEILETRPTRP3BB283 - 289265 - 271
3181ILEILETRPTRP3CC283 - 289265 - 271
3281ILEILETRPTRP3DD283 - 289265 - 271
3391PHEPHETHRTHR5AA304 - 311286 - 293
3491PHEPHETHRTHR5BB304 - 311286 - 293
3591PHEPHETHRTHR5CC304 - 311286 - 293
3691PHEPHETHRTHR5DD304 - 311286 - 293
112T5AT5AT5AT5A4AJ501
212T5AT5AT5AT5A4BR502
312T5AT5AT5AT5A4CU503

NCS ensembles :
ID
1
2

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Components

#1: Protein
Thymidine kinase /


Mass: 37013.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equid herpesvirus 4 (Equine herpesvirus 4)
Genus: Varicellovirus / Strain: 1942 / Gene: TK / Plasmid: pUT699 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C41 (DE3) / References: UniProt: P24425, thymidine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-T5A / P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE


Mass: 891.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H30N7O23P5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, MES, Dioxane, pH 6.5, Vapor Diffusion, Hanging drop, microseeding, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MMES1reservoirpH6.5
21.2 Mammonium sulfate1reservoir
35 %dioxane1reservoir
45.5 mg/mlenzyme1drop
51.0 mMTMP1drop
62.0 mMADP1drop
725 mMHEPES1droppH7.0
85 mM1dropMgSO4
95 mMdithiothreitol1drop
10100 mM1dropKCl
115 %glycerol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionHighest resolution: 3.02 Å / Num. obs: 31559
Reflection
*PLUS
Highest resolution: 3 Å / Num. all: 613603 / % possible obs: 96.8 % / Rmerge(I) obs: 0.118
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1P72

1p72


Resolution: 3.02→29.58 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.802 / SU B: 22.349 / SU ML: 0.416 / Cross valid method: THROUGHOUT / ESU R Free: 0.585 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29773 2988 9.8 %RANDOM
Rwork0.20177 ---
all0.21108 27616 --
obs0.21108 27616 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.272 Å2
Baniso -1Baniso -2Baniso -3
1-4.44 Å20 Å20 Å2
2---1.87 Å20 Å2
3----2.57 Å2
Refinement stepCycle: LAST / Resolution: 3.02→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10157 0 392 155 10704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02110759
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.99314728
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74751315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.21677
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027904
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.25262
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2457
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.79926563
X-RAY DIFFRACTIONr_mcangle_it1.443310539
X-RAY DIFFRACTIONr_scbond_it0.78924196
X-RAY DIFFRACTIONr_scangle_it1.27234189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A412tight positional0.060.05
12B412tight positional0.050.05
13C412tight positional0.060.05
14D412tight positional0.060.05
11A32medium positional0.320.5
12B32medium positional0.250.5
13C32medium positional0.430.5
14D32medium positional0.420.5
21A78medium positional0.260.5
22B78medium positional0.210.5
23C78medium positional0.210.5
11A453loose positional0.45
12B453loose positional0.395
13C453loose positional0.465
14D453loose positional0.475
11A412tight thermal0.090.5
12B412tight thermal0.10.5
13C412tight thermal0.110.5
14D412tight thermal0.110.5
11A32medium thermal1.022
12B32medium thermal0.812
13C32medium thermal1.012
14D32medium thermal1.972
21A78medium thermal0.422
22B78medium thermal0.342
23C78medium thermal0.312
11A453loose thermal1.5110
12B453loose thermal1.510
13C453loose thermal1.5610
14D453loose thermal1.8610
LS refinement shellResolution: 3.017→3.095 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 189
Rwork0.258 1724
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.604

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