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- PDB-9o57: Crystal structure of Thymidylate kinase (Tmk) from Klebsiella aer... -

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Basic information

Entry
Database: PDB / ID: 9o57
TitleCrystal structure of Thymidylate kinase (Tmk) from Klebsiella aerogenes.
ComponentsThymidylate kinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Klebsiella / Thymidylate kinase
Function / homology
Function and homology information


dTMP kinase / dTMP kinase activity / dUDP biosynthetic process / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding / cytosol
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Thymidylate kinase (Tmk) from Klebsiella aerogenes.
Authors: Liu, L. / Lovell, S. / Seibold, S. / Battaile, K.P.
History
DepositionApr 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7474
Polymers49,6772
Non-polymers712
Water00
1
A: Thymidylate kinase
hetero molecules

B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7474
Polymers49,6772
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area2620 Å2
ΔGint-38 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.407, 75.450, 76.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thymidylate kinase / dTMP kinase


Mass: 24838.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: tmk, CWM85_24435, N5C89_07930, NP224_17505 / Plasmid: KlaeA.01628.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J2I384, dTMP kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN
Has protein modificationN

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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: 1.92 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PACT B2: 0.10 M MIB buffer, pH 5.0, 25% PEG 1500. KlaeA.01628.a.B1.PW39187 at 19.7 mg/mL. plate 19509 well B2 drop 2, 2mM UMP added to the protein prior to crystallization but ligand is not ...Details: PACT B2: 0.10 M MIB buffer, pH 5.0, 25% PEG 1500. KlaeA.01628.a.B1.PW39187 at 19.7 mg/mL. plate 19509 well B2 drop 2, 2mM UMP added to the protein prior to crystallization but ligand is not bound. Puck: PSL-0313, Cryo: 0.10M MIB buffer, pH 5.0, 35% PEG 1500.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 15, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.85→19.46 Å / Num. obs: 9361 / % possible obs: 99.7 % / Redundancy: 8.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.056 / Rrim(I) all: 0.168 / Χ2: 0.99 / Net I/σ(I): 10.1 / Num. measured all: 79766
Reflection shellResolution: 2.85→3 Å / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 1.281 / Num. measured all: 11261 / Num. unique obs: 1348 / CC1/2: 0.699 / Rpim(I) all: 0.46 / Rrim(I) all: 1.364 / Χ2: 0.99 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIXdev_5660refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→19.46 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 499 5.35 %
Rwork0.2378 --
obs0.2396 9327 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 2 0 2893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042928
X-RAY DIFFRACTIONf_angle_d0.6643968
X-RAY DIFFRACTIONf_dihedral_angle_d12.9611089
X-RAY DIFFRACTIONf_chiral_restr0.041477
X-RAY DIFFRACTIONf_plane_restr0.007510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.140.33361150.30652176X-RAY DIFFRACTION100
3.14-3.590.28991160.2772182X-RAY DIFFRACTION100
3.59-4.510.26551170.22092193X-RAY DIFFRACTION100
4.51-19.460.25091510.21852277X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.636-1.64290.01713.40541.36940.7452-0.0674-0.47150.44140.4281-0.5278-0.1866-0.88940.8387-0.0080.65580.0183-0.01740.5321-0.01360.5499-8.30511.663934.1776
21.0620.55240.76440.76340.5840.61730.05591.160.6518-0.65350.3588-0.5435-1.0731-0.33110.00110.6758-0.04870.0070.60280.03550.6761-0.86443.565235.2603
31.0775-0.9848-0.96941.63911.20550.97130.3430.0210.3149-0.0803-0.1076-0.0473-0.98020.0280.00080.4733-0.04820.05680.56990.00350.424513.11590.905218.7456
41.77111.55140.3451.57850.01040.3193-0.17360.06-0.52370.46230.32340.3141-0.10080.7844-0.03010.4218-0.01610.04390.6763-0.05870.4642.8132-7.272530.9523
51.6043-0.08660.3530.1170.42331.89450.36370.3668-0.01590.1596-0.04670.00940.07030.4724-0.00030.56930.1095-0.09870.6676-0.13470.5075-11.5073-2.435415.5494
60.7288-0.35-0.45660.586-0.60781.8392-0.0765-0.2156-0.094-0.12460.19830.0479-0.124-0.3035-0.00020.4355-0.019-0.08080.4825-0.05040.6168-16.799-2.437531.3238
72.22780.58820.83252.3391-0.63440.76570.0918-0.0334-0.61960.0899-0.40780.55040.5115-0.1346-0.00540.5207-0.03940.05940.56080.0280.5294-1.863713.825543.0424
81.1223-0.0383-1.38741.2067-0.45721.7950.0063-0.68440.0950.0798-0.0260.14240.154-0.5635-0.00190.57190.0427-0.07110.63970.03440.486411.77732.403359.6683
91.34250.15380.65562.6219-0.07161.5051-0.33310.22920.6491-0.16890.4743-0.3593-0.09630.7985-0.07230.38450.1219-0.02560.3097-0.06030.554110.224714.265447.2904
100.3597-0.19130.95473.58330.3592.66590.3307-0.33730.37990.5167-0.42510.3484-0.3875-0.0464-0.00040.4773-0.0930.05510.4747-0.10420.6022-3.597122.875651.8459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 134 )
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 211 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 44 )
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 84 )
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 127 )
10X-RAY DIFFRACTION10chain 'B' and (resid 128 through 211 )

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