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- PDB-9od6: Crystal structure of nucleoside-diphosphate kinase from Cryptospo... -

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Basic information

Entry
Database: PDB / ID: 9od6
TitleCrystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with citrate
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
CITRIC ACID / nucleoside-diphosphate kinase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 from Cryptosporidium parvum in complex with citrate
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 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)53,4136
Polymers52,8373
Non-polymers5763
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint5 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.775, 69.775, 314.836
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-382-

HOH

21C-376-

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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.09 Å3/Da / Density % sol: 41.25 %
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. Citrate acquired from the crystallant. plate Liu-S-177 D2, Puck: PSL-0604, Cryo: 35% ...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. Citrate acquired from the crystallant. plate Liu-S-177 D2, Puck: PSL-0604, Cryo: 35% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5

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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: 1.45→47.93 Å / Num. obs: 81948 / % possible obs: 100 % / Redundancy: 38.9 % / CC1/2: 1 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.022 / Rrim(I) all: 0.136 / Χ2: 1.03 / Net I/σ(I): 20.2 / Num. measured all: 3188737
Reflection shellResolution: 1.45→1.49 Å / % possible obs: 100 % / Redundancy: 40.9 % / Rmerge(I) obs: 2.949 / Num. measured all: 242693 / Num. unique obs: 5933 / CC1/2: 0.69 / Rpim(I) all: 0.465 / Rrim(I) all: 2.985 / Χ2: 0.84 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(dev_5438: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→47.93 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.168 4131 5.05 %
Rwork0.1321 --
obs0.1339 81770 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 39 457 3993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083731
X-RAY DIFFRACTIONf_angle_d0.9675062
X-RAY DIFFRACTIONf_dihedral_angle_d14.9691479
X-RAY DIFFRACTIONf_chiral_restr0.074551
X-RAY DIFFRACTIONf_plane_restr0.009660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.34381470.26392511X-RAY DIFFRACTION100
1.47-1.480.27391390.23632551X-RAY DIFFRACTION100
1.48-1.50.3071310.20812500X-RAY DIFFRACTION100
1.5-1.520.22281440.17782564X-RAY DIFFRACTION100
1.52-1.540.22421250.16512504X-RAY DIFFRACTION100
1.54-1.560.2051010.1632580X-RAY DIFFRACTION100
1.56-1.580.23681410.15072548X-RAY DIFFRACTION100
1.58-1.610.21061280.14162533X-RAY DIFFRACTION100
1.61-1.630.21411220.1372565X-RAY DIFFRACTION100
1.63-1.660.18611290.12822553X-RAY DIFFRACTION100
1.66-1.690.17081350.12592541X-RAY DIFFRACTION100
1.69-1.720.18431370.12582532X-RAY DIFFRACTION100
1.72-1.750.22171340.12872583X-RAY DIFFRACTION100
1.75-1.790.20291370.13282553X-RAY DIFFRACTION100
1.79-1.830.17891560.12522522X-RAY DIFFRACTION100
1.83-1.870.17881460.1272526X-RAY DIFFRACTION100
1.87-1.920.18821530.1292562X-RAY DIFFRACTION100
1.92-1.970.17771240.13112580X-RAY DIFFRACTION100
1.97-2.030.15741500.11772572X-RAY DIFFRACTION100
2.03-2.090.17821300.11632573X-RAY DIFFRACTION100
2.09-2.170.151490.1132601X-RAY DIFFRACTION100
2.17-2.250.15141420.11032590X-RAY DIFFRACTION100
2.25-2.360.14641400.11152577X-RAY DIFFRACTION100
2.36-2.480.14561370.11782618X-RAY DIFFRACTION100
2.48-2.630.16281440.12662610X-RAY DIFFRACTION100
2.63-2.840.1541510.13142623X-RAY DIFFRACTION100
2.84-3.120.15981220.13692682X-RAY DIFFRACTION100
3.12-3.580.1581400.12962684X-RAY DIFFRACTION100
3.58-4.50.13031400.11682750X-RAY DIFFRACTION100
4.5-47.930.1781570.15592951X-RAY DIFFRACTION100

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