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- PDB-9oak: Crystal structure of nucleoside-diphosphate kinase from Cryptospo... -

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Basic information

Entry
Database: PDB / ID: 9oak
TitleCrystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with cytidine-5'-diphosphate and cytidine-5'-triphosphate
Componentsnucleoside-diphosphate kinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process
Similarity search - Function
Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
CYTIDINE-5'-DIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / nucleoside-diphosphate kinase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 nucleoside-diphosphate kinase Cryptosporidium parvum in complex with cytidine-5'-diphosphate and cytidine-5'-triphosphate
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 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: nucleoside-diphosphate kinase
B: nucleoside-diphosphate kinase
C: nucleoside-diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0127
Polymers53,0773
Non-polymers9354
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-33 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.734, 69.734, 316.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

21C-374-

HOH

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Components

#1: Protein nucleoside-diphosphate kinase


Mass: 17692.340 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd4_1940 / Plasmid: CrpaA.01302.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5CR64, nucleoside-diphosphate kinase
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Berkeley F12: 25% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystals soaked for 4 hours in 10mM ligand, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, ...Details: Berkeley F12: 25% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystals soaked for 4 hours in 10mM ligand, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. Subunit A contains partially occupied CTP and HIP from reaction. Subunit C contains partially occupied CDP and HIP. plate Liu-S-177 D2, Puck: PSL-0503, Cryo: direct from soaking solution

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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: Apr 5, 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: 1.61→47.99 Å / Num. obs: 60534 / % possible obs: 100 % / Redundancy: 16.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.024 / Rrim(I) all: 0.102 / Χ2: 0.94 / Net I/σ(I): 19.8 / Num. measured all: 1023118
Reflection shellResolution: 1.61→1.65 Å / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.869 / Num. measured all: 32252 / Num. unique obs: 4362 / CC1/2: 0.765 / Rpim(I) all: 0.335 / Rrim(I) all: 0.934 / Χ2: 0.68 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(dev_5669: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→47.99 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1715 3014 4.99 %
Rwork0.1449 --
obs0.1462 60366 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 56 429 4004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093765
X-RAY DIFFRACTIONf_angle_d1.0475120
X-RAY DIFFRACTIONf_dihedral_angle_d16.4091517
X-RAY DIFFRACTIONf_chiral_restr0.058563
X-RAY DIFFRACTIONf_plane_restr0.011655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.640.29061520.27442526X-RAY DIFFRACTION100
1.64-1.660.24331270.22382575X-RAY DIFFRACTION100
1.66-1.690.2269970.1912548X-RAY DIFFRACTION100
1.69-1.720.22161340.17492548X-RAY DIFFRACTION100
1.72-1.750.21751280.16432567X-RAY DIFFRACTION100
1.75-1.790.19321340.15252566X-RAY DIFFRACTION100
1.79-1.830.19161310.14722569X-RAY DIFFRACTION100
1.83-1.870.16781320.15022527X-RAY DIFFRACTION100
1.87-1.920.17441560.15182547X-RAY DIFFRACTION100
1.92-1.970.17921330.1532572X-RAY DIFFRACTION100
1.97-2.030.17241570.132553X-RAY DIFFRACTION100
2.03-2.090.16061280.12712591X-RAY DIFFRACTION100
2.09-2.170.14381390.12422592X-RAY DIFFRACTION100
2.17-2.260.16741400.1282583X-RAY DIFFRACTION100
2.26-2.360.17851440.12952576X-RAY DIFFRACTION100
2.36-2.480.15571290.13722625X-RAY DIFFRACTION100
2.48-2.640.18471450.1472613X-RAY DIFFRACTION100
2.64-2.840.1591130.14582658X-RAY DIFFRACTION100
2.84-3.130.15831220.1442674X-RAY DIFFRACTION100
3.13-3.580.16581490.13782671X-RAY DIFFRACTION100
3.58-4.510.1361600.12352729X-RAY DIFFRACTION100
4.51-47.990.19261640.16332942X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.0974 Å / Origin y: 28.7826 Å / Origin z: 14.1556 Å
111213212223313233
T0.1216 Å20.0247 Å20.0001 Å2-0.1407 Å20.0079 Å2--0.1084 Å2
L0.4051 °2-0.0501 °20.0078 °2-0.2672 °20.0548 °2--0.3715 °2
S0.0075 Å °0.0539 Å °0.0099 Å °-0.0521 Å °-0.014 Å °0.0085 Å °0.0274 Å °0.0281 Å °0.0069 Å °
Refinement TLS groupSelection details: all

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