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- PDB-3ld9: Crystal structure of thymidylate kinase from Ehrlichia chaffeensi... -

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Basic information

Entry
Database: PDB / ID: 3ld9
TitleCrystal structure of thymidylate kinase from Ehrlichia chaffeensis at 2.15A resolution
ComponentsThymidylate kinase
KeywordsTRANSFERASE / SSGCID / NIH / NIAID / SBRI / UW / Emerald Biostructures / Ehrlichia chaffeensis / thymidylate kinase / ALS collaborative crystallography / ATP-binding / Kinase / Nucleotide biosynthesis / Nucleotide-binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEhrlichia chaffeensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of thymidylate kinase from Ehrlichia chaffeensis.
Authors: Leibly, D.J. / Abendroth, J. / Bryan, C.M. / Sankaran, B. / Kelley, A. / Barrett, L.K. / Stewart, L. / Van Voorhis, W.C.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 6, 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.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)102,56110
Polymers102,0524
Non-polymers5086
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-109 kcal/mol
Surface area32000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.170, 144.820, 146.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHE6AA-2 - 5319 - 74
21PROPROPHEPHE6BB-2 - 5319 - 74
31PROPROPHEPHE6CC-2 - 5319 - 74
41PROPROPHEPHE6DD-2 - 5319 - 74
12ASPASPGLNGLN4AA59 - 20080 - 221
22ASPASPGLNGLN4BB59 - 20080 - 221
32ASPASPGLNGLN4CC59 - 20080 - 221
42ASPASPGLNGLN4DD59 - 20080 - 221

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Components

#1: Protein
Thymidylate kinase / dTMP kinase


Mass: 25513.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ehrlichia chaffeensis (bacteria) / Strain: ARKANSAS / Gene: tmk, ECH_0229 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GHN3, dTMP kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MD PACT SCREEN G8: 100MM BIS-TRIS-PROPANE PH 7.5, 200MM NA-SULPHATE, 20% PEG 3350; EHCHA.01616.A AT 25.5MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9744 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2009 / Details: Single crystal, cylindrically bent, Si(220)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97741
20.97441
ReflectionResolution: 2.15→50 Å / Num. all: 46727 / Num. obs: 46708 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.84
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PBR MODIFIED WITH CCP4 PROGRAM CHAINSAW

2pbr


Resolution: 2.15→46.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.683 / SU ML: 0.126 / Isotropic thermal model: ISOTROPIC, TLS / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 2354 5 %RANDOM
Rwork0.18656 ---
obs0.18883 44279 99.97 %-
all-46727 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.523 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å20 Å2
2---2.03 Å2-0 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5700 0 28 301 6029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225917
X-RAY DIFFRACTIONr_bond_other_d0.0010.023909
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.968021
X-RAY DIFFRACTIONr_angle_other_deg0.90639541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03524.25280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.267151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6331531
X-RAY DIFFRACTIONr_chiral_restr0.0760.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.53620
X-RAY DIFFRACTIONr_mcbond_other0.2081.51497
X-RAY DIFFRACTIONr_mcangle_it1.29525859
X-RAY DIFFRACTIONr_scbond_it2.11232297
X-RAY DIFFRACTIONr_scangle_it3.364.52151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1420medium positional0.370.5
2B1420medium positional0.350.5
3C1420medium positional0.410.5
4D1420medium positional0.380.5
1A658loose positional0.345
2B658loose positional0.415
3C658loose positional0.775
4D658loose positional0.425
1A1420medium thermal0.762
2B1420medium thermal0.762
3C1420medium thermal0.872
4D1420medium thermal0.882
1A658loose thermal0.7610
2B658loose thermal0.7510
3C658loose thermal0.7810
4D658loose thermal0.8310
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 175 -
Rwork0.205 3227 -
obs--99.88 %
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)
10.7420.6103-0.15953.1705-0.85620.7372-0.12230.0726-0.0281-0.56560.1186-0.2367-0.1035-0.01970.00380.2309-0.02990.07220.0654-0.03440.083438.3119.4955105.5522
20.82120.0927-0.00972.95230.48020.9947-0.06250.0223-0.07360.10670.02340.04070.1359-0.09810.03910.0266-0.01590.02440.0525-0.04040.089326.9225-21.4252119.5174
31.0010.5532-0.01433.424-0.95412.56550.0924-0.1571-0.23980.4891-0.1441-0.34160.45340.23840.05170.24280.0318-0.09280.11170.02330.143837.5456-1.9476146.5811
40.9801-0.1916-0.15682.08970.32651.02170.02560.08910.0602-0.0306-0.04360.0683-0.101-0.08980.01810.01380.0042-0.0120.086-0.02480.070726.864628.9106133.5254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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