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- PDB-4gmd: The crystal structure of thymidylate kinase from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 4gmd
TitleThe crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with AZT Monophosphate
ComponentsThymidylate kinase
KeywordsTransferase/Inhibitor / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / PROTEIN STRUCTURE INITIATIVE / TRANSFERASE / Transferase-Inhibitor complex
Function / homology
Function and homology information


dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding / cytosol / cytoplasm
Similarity search - Function
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
3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsTan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex with AZT Monophosphate
Authors: Tan, K. / Joachimiak, G. / Jedrzejczak, R. / Sacchettini, J. / Joachimiak, A.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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: Thymidylate kinase
B: Thymidylate kinase
C: Thymidylate kinase
D: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,55218
Polymers93,6344
Non-polymers1,91814
Water5,621312
1
A: Thymidylate kinase
C: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7108
Polymers46,8172
Non-polymers8936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-39 kcal/mol
Surface area17740 Å2
MethodPISA
2
B: Thymidylate kinase
D: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,84210
Polymers46,8172
Non-polymers1,0258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-47 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.500, 123.404, 73.920
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. The chains A and B, C and D may form dimers, respectively.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thymidylate kinase / dTMP kinase


Mass: 23408.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2962, tmk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9HZN8, dTMP kinase

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Non-polymers , 5 types, 326 molecules

#2: Chemical
ChemComp-ATM / 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M CaCl2, 0.1M Tris:HCl, 20%(w/v) PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.98→34 Å / Num. all: 54559 / Num. obs: 54559 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 24.4
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2763 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E5U
Resolution: 1.98→34 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 2767 5.08 %random
Rwork0.1772 ---
all0.1797 54514 --
obs0.1797 54514 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.786 Å2 / ksol: 0.302 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7397 Å2-0 Å23.4182 Å2
2---8.035 Å2-0 Å2
3---0.2953 Å2
Refinement stepCycle: LAST / Resolution: 1.98→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6172 0 117 312 6601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076379
X-RAY DIFFRACTIONf_angle_d1.0028643
X-RAY DIFFRACTIONf_dihedral_angle_d14.0362428
X-RAY DIFFRACTIONf_chiral_restr0.065965
X-RAY DIFFRACTIONf_plane_restr0.0051155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9798-2.01390.29251310.23362596X-RAY DIFFRACTION98
2.0139-2.05050.29121420.21522561X-RAY DIFFRACTION100
2.0505-2.090.23541380.22122563X-RAY DIFFRACTION100
2.09-2.13260.30731180.20792594X-RAY DIFFRACTION100
2.1326-2.1790.28521340.20632597X-RAY DIFFRACTION100
2.179-2.22970.27581490.19992582X-RAY DIFFRACTION100
2.2297-2.28540.23371360.18832567X-RAY DIFFRACTION100
2.2854-2.34720.27061340.19012617X-RAY DIFFRACTION100
2.3472-2.41620.28751540.19772541X-RAY DIFFRACTION100
2.4162-2.49420.26861290.19962612X-RAY DIFFRACTION100
2.4942-2.58330.26691360.19642579X-RAY DIFFRACTION100
2.5833-2.68670.2491420.20872547X-RAY DIFFRACTION100
2.6867-2.80890.26211430.20522629X-RAY DIFFRACTION100
2.8089-2.9570.26181320.20712606X-RAY DIFFRACTION100
2.957-3.14210.26691350.19372576X-RAY DIFFRACTION100
3.1421-3.38450.23461450.18372587X-RAY DIFFRACTION100
3.3845-3.72470.21811480.1672594X-RAY DIFFRACTION100
3.7247-4.26280.1941400.14652570X-RAY DIFFRACTION100
4.2628-5.36730.14371490.13552605X-RAY DIFFRACTION100
5.3673-34.04180.21431320.16962624X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.1222-0.35871.38685.1840.57891.9624-0.0991-0.4428-0.08650.06670.24060.23320.0216-0.248-0.10050.50390.04920.01220.38910.03050.334915.4043-54.383915.518
20.56980.12760.26922.83150.39571.53640.01430.0245-0.0489-0.3743-0.03810.04280.04640.02750.02020.28090.02710.00190.25890.0130.274118.3806-39.527623.2638
31.7416-0.93520.6310.5307-0.81876.90730.4004-0.7654-0.76350.1806-0.1010.5190.3933-1.1774-0.1810.5022-0.0587-0.00380.63770.13310.84441.2117-43.649830.5451
44.4791-0.3783-1.37293.97681.34697.07180.57760.41490.1869-0.6647-0.23270.9845-0.5165-0.94630.05130.51820.1885-0.26560.3771-0.0050.43222.9236-37.025116.8532
51.3835-1.21220.61645.12360.44682.46490.42580.2927-0.0009-1.7739-0.2720.5078-0.27130.23330.02110.89340.1289-0.08410.41590.01850.44210.9372-51.8967.2641
66.91831.07931.36443.50011.02733.8871-0.3930.7080.0290.21320.4324-0.2511-0.10740.3893-0.00870.32480.0452-0.00590.37880.0180.348133.1612-29.5194-5.3736
75.04563.50061.67596.04411.98012.1055-0.10810.1159-0.5416-0.25480.1917-0.8534-0.25460.2569-0.0010.48250.04710.04670.32950.01560.398132.4863-33.6658-16.2996
80.77070.26870.28352.73451.82053.036-0.00350.1871-0.0281-0.68670.0584-0.4809-0.34520.2789-0.00770.40250.10040.07930.36240.03770.355729.5431-14.7693-4.2889
90.81730.1558-0.16851.61170.55770.70950.08020.1477-0.1561-0.1356-0.0649-0.0470.0230.0042-0.02230.31210.07150.01980.3510.01190.277228.4692-22.131.6518
101.4114-0.23620.5182.0250.85732.36510.07710.0813-0.10790.32210.01460.00820.4306-0.0034-0.09720.39640.04930.02620.3120.01880.352829.0411-28.15756.1517
110.9541-0.558-0.74440.9878-0.45731.69340.02360.93931.24890.05-0.0174-0.3757-0.4528-0.0007-0.18380.3126-0.1150.14670.7265-0.05960.92745.8837-16.6664-0.6161
124.06512.6415-0.13576.28280.57662.16760.3904-0.37330.24650.5633-0.3833-0.53140.19540.78630.03790.32450.1133-0.02570.52990.00760.484544.1124-26.91525.8513
135.13850.423-2.59763.7581-0.14026.57530.20060.0415-0.6070.27520.0976-0.22150.3002-0.1375-0.39450.39110.0764-0.00730.4556-0.00520.466339.6947-36.9787-1.7781
147.77750.24042.04924.34040.7286.43040.1474-0.0596-0.35031.13910.6124-0.2411.31460.6735-0.76940.77680.1677-0.14050.3963-0.07790.578934.8865-41.3401-10.4955
155.6847-0.21381.11381.98510.32933.5847-0.0484-0.4304-0.37030.17760.1393-0.1609-0.1953-0.24070.02430.462-0.0804-0.05910.29820.00590.246528.1263-14.801244.5601
164.1667-3.6551-1.03435.40381.48351.0507-0.5521-0.4163-0.23621.19770.37080.0950.09030.15330.19750.56210.0036-0.0180.4384-0.00240.360125.0699-10.112154.6819
171.0434-0.66640.01592.35860.35641.5629-0.1166-0.0532-0.00820.22740.0314-0.07250.0058-0.01540.08740.2142-0.0065-0.02590.28970.01610.278221.8299-25.557640.1985
181.42080.1825-0.56691.86640.06632.73050.0445-0.00580.1499-0.2358-0.1467-0.2176-0.37680.37610.09070.32160.005-0.02540.31350.03950.328729.3471-19.081732.8723
193.512-0.01110.98811.08531.44792.21640.3493-0.7356-0.27890.6872-0.1035-0.76520.02360.58050.20860.4493-0.0507-0.14810.75950.04110.734639.4264-31.137743.5317
202.9229-1.73130.66144.00080.45271.59310.09440.13220.19520.0933-0.2763-0.894-0.15321.31840.05960.3036-0.1173-0.07010.72380.07860.512441.3413-18.723636.5274
213.2446-0.46093.19581.54810.06226.8706-0.28690.07640.509-0.3710.0185-0.2075-0.62760.4310.20630.5176-0.1226-0.10130.58660.00950.42936.172-8.060342.5155
226.3701-1.07131.7322.8393-0.84853.7841-0.10190.28830.1982-0.13170.2371-0.4811-0.64290.4417-0.01450.5285-0.10060.05020.4792-0.12350.552228.466-2.581449.2465
232.34240.6857-0.06832.91280.4351.39940.0970.19920.2532-0.0527-0.10850.190.1828-0.15670.03610.348-0.00860.02980.30930.01350.336218.996710.757221.2351
241.01780.0225-0.12282.31621.46511.4048-0.00820.15880.0718-0.353-0.0239-0.0227-0.30680.0089-0.01220.29040.04950.03680.30740.04820.295524.5135-1.875510.6741
252.0504-0.64640.02654.1476-0.22162.2129-0.0009-0.0187-0.04390.29020.0110.2030.12430.03490.05410.27430.02750.04520.27710.02790.271716.8397-7.975118.1653
264.0229-1.794-1.55812.21770.69752.62890.34080.81410.7677-0.1205-0.63580.2687-0.2932-1.05450.15870.3890.0885-0.07830.58820.00720.58417.2445-1.02724.5233
274.149-0.05991.9023.311.74799.75050.1225-0.14220.35650.1305-0.15531.10110.4944-1.2622-0.06670.28860.01370.09860.3960.00430.58684.6927-4.928617.0111
282.8116-2.1961.49244.4218-1.31431.951-0.4732-0.4977-0.03150.58230.2007-0.12720.1083-0.04570.14810.40350.14950.06390.40720.01310.35228.99763.540526.0519
294.3897-1.33381.21523.7842-1.02283.5843-0.2572-0.5569-0.02880.32940.15490.1863-0.254-0.36620.11040.4357-0.02720.04990.3279-0.02880.268115.451611.623430.1764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:30)
2X-RAY DIFFRACTION2chain 'A' and (resseq 31:136)
3X-RAY DIFFRACTION3chain 'A' and (resseq 137:159)
4X-RAY DIFFRACTION4chain 'A' and (resseq 160:177)
5X-RAY DIFFRACTION5chain 'A' and (resseq 178:209)
6X-RAY DIFFRACTION6chain 'B' and (resseq 2:15)
7X-RAY DIFFRACTION7chain 'B' and (resseq 16:30)
8X-RAY DIFFRACTION8chain 'B' and (resseq 31:62)
9X-RAY DIFFRACTION9chain 'B' and (resseq 63:112)
10X-RAY DIFFRACTION10chain 'B' and (resseq 113:136)
11X-RAY DIFFRACTION11chain 'B' and (resseq 137:159)
12X-RAY DIFFRACTION12chain 'B' and (resseq 160:176)
13X-RAY DIFFRACTION13chain 'B' and (resseq 177:189)
14X-RAY DIFFRACTION14chain 'B' and (resseq 190:208)
15X-RAY DIFFRACTION15chain 'C' and (resseq 2:15)
16X-RAY DIFFRACTION16chain 'C' and (resseq 16:30)
17X-RAY DIFFRACTION17chain 'C' and (resseq 31:95)
18X-RAY DIFFRACTION18chain 'C' and (resseq 96:136)
19X-RAY DIFFRACTION19chain 'C' and (resseq 137:159)
20X-RAY DIFFRACTION20chain 'C' and (resseq 160:176)
21X-RAY DIFFRACTION21chain 'C' and (resseq 177:189)
22X-RAY DIFFRACTION22chain 'C' and (resseq 190:209)
23X-RAY DIFFRACTION23chain 'D' and (resseq 2:30)
24X-RAY DIFFRACTION24chain 'D' and (resseq 31:95)
25X-RAY DIFFRACTION25chain 'D' and (resseq 96:136)
26X-RAY DIFFRACTION26chain 'D' and (resseq 137:159)
27X-RAY DIFFRACTION27chain 'D' and (resseq 160:176)
28X-RAY DIFFRACTION28chain 'D' and (resseq 177:189)
29X-RAY DIFFRACTION29chain 'D' and (resseq 190:209)

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