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- PDB-9o9r: Crystal structure of nucleoside-diphosphate kinase Cryptosporidiu... -

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Basic information

Entry
Database: PDB / ID: 9o9r
TitleCrystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum
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 (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
nucleoside-diphosphate kinase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.31 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
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 18, 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

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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)53,89414
Polymers52,8373
Non-polymers1,05711
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-108 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.985, 69.985, 315.415
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-384-

HOH

21A-459-

HOH

31C-496-

HOH

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Components

#1: Protein nucleoside-diphosphate kinase


Mass: 17612.361 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Index HT C6: 1.5M ammonium sufate, 0.1M sodium chloride, 0.1 M Bis-Tris pH 6.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. plate 19658 C6 drop 1, Puck: PSL-0601, Cryo: Paratone-N and parafin oil (1:1)

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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 2, 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: 1.31→48.05 Å / Num. obs: 111176 / % possible obs: 100 % / Redundancy: 36.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.026 / Rrim(I) all: 0.158 / Χ2: 0.98 / Net I/σ(I): 22.9 / Num. measured all: 4047371
Reflection shellResolution: 1.31→1.34 Å / % possible obs: 99.6 % / Redundancy: 20.9 % / Rmerge(I) obs: 1.304 / Num. measured all: 168206 / Num. unique obs: 8057 / CC1/2: 0.564 / Rpim(I) all: 0.289 / Rrim(I) all: 1.336 / Χ2: 0.76 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156: ???)refinement
Aimlessdata scaling
XDSdata reduction
SHELXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 1.31→48.05 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1871 5522 4.98 %
Rwork0.1475 --
obs0.1494 110988 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 55 574 4126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083700
X-RAY DIFFRACTIONf_angle_d0.9335019
X-RAY DIFFRACTIONf_dihedral_angle_d14.9091432
X-RAY DIFFRACTIONf_chiral_restr0.075546
X-RAY DIFFRACTIONf_plane_restr0.01643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.320.35141840.27243437X-RAY DIFFRACTION99
1.32-1.340.27151930.23453405X-RAY DIFFRACTION100
1.34-1.360.30951930.22443435X-RAY DIFFRACTION100
1.36-1.370.25831700.21243497X-RAY DIFFRACTION100
1.37-1.390.2731730.21183431X-RAY DIFFRACTION100
1.39-1.410.27551890.19123454X-RAY DIFFRACTION100
1.41-1.430.25271830.18373444X-RAY DIFFRACTION100
1.43-1.450.23611930.17723442X-RAY DIFFRACTION100
1.45-1.480.21341940.17223447X-RAY DIFFRACTION100
1.48-1.50.23441660.1643467X-RAY DIFFRACTION100
1.5-1.530.21761930.16063481X-RAY DIFFRACTION100
1.53-1.550.21721750.16073475X-RAY DIFFRACTION100
1.55-1.580.20051730.15023472X-RAY DIFFRACTION100
1.58-1.620.19391970.14393445X-RAY DIFFRACTION100
1.62-1.650.20391790.143477X-RAY DIFFRACTION100
1.65-1.690.20462170.14023447X-RAY DIFFRACTION100
1.69-1.730.18692120.13463466X-RAY DIFFRACTION100
1.73-1.780.17441750.13423509X-RAY DIFFRACTION100
1.78-1.830.20391930.13243477X-RAY DIFFRACTION100
1.83-1.890.17731830.13213535X-RAY DIFFRACTION100
1.89-1.960.16121720.12953512X-RAY DIFFRACTION100
1.96-2.040.16091790.12463511X-RAY DIFFRACTION100
2.04-2.130.1591700.12223562X-RAY DIFFRACTION100
2.13-2.240.16621860.12293529X-RAY DIFFRACTION100
2.24-2.380.14881690.12663574X-RAY DIFFRACTION100
2.38-2.560.1561760.13043585X-RAY DIFFRACTION100
2.56-2.820.15391970.14033589X-RAY DIFFRACTION100
2.82-3.230.1771590.15383659X-RAY DIFFRACTION100
3.23-4.070.14091770.13183729X-RAY DIFFRACTION100
4.07-48.050.19612020.15553973X-RAY DIFFRACTION100

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