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- PDB-9pg0: Crystal structure of nucleoside-diphosphate kinase Cryptosporidiu... -

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Basic information

Entry
Database: PDB / ID: 9pg0
TitleCrystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum in complex with AMP
Componentsnucleoside-diphosphate kinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / nucleoside-diphosphate kinase
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
ADENOSINE MONOPHOSPHATE / 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 Cryptosporidium parvum in complex with AMP
Authors: Enayati, P. / Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionJul 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 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)54,2267
Polymers52,8373
Non-polymers1,3894
Water10,034557
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.923, 69.923, 315.876
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-390-

HOH

21A-442-

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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Berkeley F12: 35% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystal soaked overnight in 10mM AMP in crystallant. plate Liu-S-177 D2, Puck: PSL- ...Details: Berkeley F12: 35% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. CrpaA.01302.a.B2.PW39348 at 8.9 mg/mL. Crystal soaked overnight in 10mM AMP in crystallant. plate Liu-S-177 D2, Puck: PSL-0201, 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: May 25, 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→48.05 Å / Num. obs: 81188 / % possible obs: 98.5 % / Redundancy: 16.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.022 / Rrim(I) all: 0.093 / Χ2: 1.02 / Net I/σ(I): 18.3 / Num. measured all: 1320442
Reflection shellResolution: 1.45→1.47 Å / % possible obs: 90.1 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.662 / Num. measured all: 20716 / Num. unique obs: 3558 / CC1/2: 0.748 / Rpim(I) all: 0.295 / Rrim(I) all: 0.728 / Χ2: 1.02 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(2.0_5740: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→48.05 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1551 4114 5.08 %
Rwork0.1234 --
obs0.125 81019 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 92 557 4155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083737
X-RAY DIFFRACTIONf_angle_d1.1295067
X-RAY DIFFRACTIONf_dihedral_angle_d16.8891454
X-RAY DIFFRACTIONf_chiral_restr0.077551
X-RAY DIFFRACTIONf_plane_restr0.01644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.25791480.22412304X-RAY DIFFRACTION89
1.47-1.480.2991240.21142401X-RAY DIFFRACTION90
1.48-1.50.26451350.22403X-RAY DIFFRACTION92
1.5-1.520.21031410.17152490X-RAY DIFFRACTION94
1.52-1.540.21691280.15382473X-RAY DIFFRACTION95
1.54-1.570.1871060.13422566X-RAY DIFFRACTION96
1.57-1.590.19851420.12212605X-RAY DIFFRACTION97
1.59-1.610.1571310.10692595X-RAY DIFFRACTION99
1.61-1.640.16251260.09682653X-RAY DIFFRACTION100
1.64-1.670.13821330.09522690X-RAY DIFFRACTION100
1.67-1.70.13231400.08982639X-RAY DIFFRACTION100
1.7-1.730.13191530.09382644X-RAY DIFFRACTION100
1.73-1.770.15451300.1052654X-RAY DIFFRACTION100
1.77-1.810.15561480.11272670X-RAY DIFFRACTION100
1.81-1.850.14661600.11522674X-RAY DIFFRACTION100
1.85-1.890.15951670.1212652X-RAY DIFFRACTION100
1.89-1.950.18071400.1322679X-RAY DIFFRACTION100
1.95-20.14251430.10812658X-RAY DIFFRACTION100
2-2.070.16511430.10392690X-RAY DIFFRACTION100
2.07-2.140.14361430.10482682X-RAY DIFFRACTION100
2.14-2.230.14321530.10832693X-RAY DIFFRACTION100
2.23-2.330.14291580.10262721X-RAY DIFFRACTION100
2.33-2.450.13091290.10812703X-RAY DIFFRACTION100
2.45-2.60.15171540.11152722X-RAY DIFFRACTION100
2.61-2.810.14171560.11582749X-RAY DIFFRACTION100
2.81-3.090.1551290.13012757X-RAY DIFFRACTION100
3.09-3.540.14811480.12792805X-RAY DIFFRACTION100
3.54-4.450.12131370.11962867X-RAY DIFFRACTION100
4.45-48.050.17511690.16423066X-RAY DIFFRACTION100

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