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- PDB-7l4a: Crystal Structure of Cytidylate kinase from Encephalitozoon cunic... -

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Basic information

Entry
Database: PDB / ID: 7l4a
TitleCrystal Structure of Cytidylate kinase from Encephalitozoon cuniculi GB-M1 in complex with two CDP molecules
ComponentsCytidylate kinase
KeywordsTRANSFERASE / SSGCID / cytidylate kinase / Encephalitozoon cuniculi / CDP / CTP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


(d)CMP kinase / CMP kinase activity / dCMP kinase activity / nucleobase-containing small molecule interconversion / ATP binding / cytosol
Similarity search - Function
Cytidylate kinase / Cytidylate kinase domain / Cytidylate 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
CYTIDINE-5'-DIPHOSPHATE / Probable cytidylate kinase
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Cytidylate kinase from Encephalitozoon cuniculi GB-M1 in complex with two CDP molecules
Authors: Abendroth, J.A. / Fox III, D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3025
Polymers26,3381
Non-polymers9644
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.520, 46.870, 53.830
Angle α, β, γ (deg.)90.000, 112.592, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cytidylate kinase / CK / Cytidine monophosphate kinase / CMP kinase


Mass: 26337.838 Da / Num. of mol.: 1 / Fragment: EncuA.01086.a.AE1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (strain GB-M1) (fungus)
Strain: GB-M1 / Gene: ECU03_1270 / Plasmid: Endua.01086.a.aE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8SS83, (d)CMP kinase
#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Optimization condition: 100mM BisTris pH 6, 200mM ammonium sulfate, 26% (w/V) PEG 3350: EucuA.01086.a.AE1.PS38633 at 56.56mg/ml + 5mM CTP + 5mM MgCl2: tray 318933 a2: cryo: 20% EG + ligands: ...Details: Optimization condition: 100mM BisTris pH 6, 200mM ammonium sulfate, 26% (w/V) PEG 3350: EucuA.01086.a.AE1.PS38633 at 56.56mg/ml + 5mM CTP + 5mM MgCl2: tray 318933 a2: cryo: 20% EG + ligands: puck akp1-5. For phasing, a crystal from MCSG1, condition D7 (20% (w/V) PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: EncuA.01086.a.AE1.PS38636 at 28.28mg/ml, tray 315976 d7) was dipped for 20sec in a solution of 4ul half saturated NaI in ethylene glycol and reservoir and directly vitrified. This crystal form could not be reproduced.

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDateDetails
RAYONIX MX-3001CCDDec 3, 2020Beryllium Lenses
RIGAKU SATURN 944+2CCDJul 15, 2020
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond [111]SINGLE WAVELENGTHMx-ray1
2RIGAKU VARIMAXSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.54181
ReflectionResolution: 1.5→50 Å / Num. obs: 35784 / % possible obs: 99.5 % / Redundancy: 4.026 % / Biso Wilson estimate: 25.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.049 / Χ2: 0.948 / Net I/σ(I): 17.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.543.1890.4482.4925620.8220.53897
1.54-1.583.8820.3653.5425670.8990.424100
1.58-1.634.1160.2834.6925020.9490.32599.7
1.63-1.684.1230.2335.5724440.9660.26899.8
1.68-1.734.1270.1986.7923550.970.22799.7
1.73-1.794.1220.1548.6922720.9810.177100
1.79-1.864.1420.11711.0422020.990.13499.6
1.86-1.944.1340.09114.0621230.9930.10499.7
1.94-2.024.1310.07117.7420190.9960.081100
2.02-2.124.1170.05821.7719540.9960.06799.5
2.12-2.244.1380.04925.1618540.9970.05699.9
2.24-2.374.1220.04327.5617410.9970.0599.5
2.37-2.544.1070.03930.2316390.9980.04599.8
2.54-2.744.0940.03732.1315540.9980.04399.7
2.74-34.0810.03435.2414170.9980.03999.6
3-3.354.0850.0337.513010.9980.03599.5
3.35-3.874.070.02940.0311240.9980.03499.6
3.87-4.744.0730.02740.819710.9990.03199.7
4.74-6.713.9960.02739.877580.9990.03199.2
6.71-503.7320.02639.974250.9980.03198.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4 4035refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.5→44.8 Å / SU ML: 0.1657 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.4856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 2003 5.6 %0
Rwork0.1482 33772 --
obs0.1507 35775 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1779 0 59 235 2073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811976
X-RAY DIFFRACTIONf_angle_d0.95412688
X-RAY DIFFRACTIONf_chiral_restr0.0586304
X-RAY DIFFRACTIONf_plane_restr0.0118365
X-RAY DIFFRACTIONf_dihedral_angle_d11.1348813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.26381280.19772341X-RAY DIFFRACTION96.82
1.54-1.580.24511390.16612396X-RAY DIFFRACTION99.92
1.58-1.630.22671280.15132420X-RAY DIFFRACTION99.96
1.63-1.680.23271560.15712403X-RAY DIFFRACTION99.84
1.68-1.740.26281310.16082425X-RAY DIFFRACTION99.92
1.74-1.810.23961390.16672386X-RAY DIFFRACTION100
1.81-1.890.21441380.15162426X-RAY DIFFRACTION99.81
1.89-1.990.22321570.14782391X-RAY DIFFRACTION99.96
1.99-2.110.21371400.14452427X-RAY DIFFRACTION99.84
2.11-2.280.16931210.14092411X-RAY DIFFRACTION99.76
2.28-2.510.18431520.14352422X-RAY DIFFRACTION99.92
2.51-2.870.18791490.16092423X-RAY DIFFRACTION99.84
2.87-3.610.18211620.14312426X-RAY DIFFRACTION99.77
3.61-44.80.15561630.13952475X-RAY DIFFRACTION99.62

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