SAXSdb — 9pfy

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1. Protein Identity and Related Structures Protein Identity & Related Structures

nucleoside-diphosphate kinase

Cryptosporidium parvum Iowa II

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 26–173 Chain B； UniProt 26–173 Chain C； UniProt 26–173	Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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 was transferred to 35% MPD, 100mM Bis-Tris, pH 5.5, 100mM sodium formate two times and then soaked with in the same solution containing 10mM ATP for 3 hours. Subunits A and C have partial occupancy of ATP and HIP in the active site. Subunit B had 100% conversion to HIP. plate Liu-S-177 D2, Puck: PSL-0105, Cryo: direct from soaking solution	Resolution 1.42 Å R-free 0.156

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9PFY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9O9R Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum Deposited 2025-04-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Not recorded	SO4 SULFATE ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；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)	Resolution 1.31 Å R-free 0.187
9OAI Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with thymidine-5'-phosphate Deposited 2025-04-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Not recorded	TMP THYMIDINE-5'-PHOSPHATE × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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. plate Liu-S-177 D2, Puck: PSL-0505, Cryo: direct from soaking solution	Resolution 1.51 Å R-free 0.163
9OAK Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with cytidine-5'-diphosphate and cytidine-5'-triphosphate Deposited 2025-04-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CTP CYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 CDP CYTIDINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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	Resolution 1.61 Å R-free 0.172
9OAN Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with with guanosine-5'-diphosphate and AMP-PNP Deposited 2025-04-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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 ANP and GDP, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. Ligands only bound if ANP is present. GDP only soaks did not produce binding. plate Liu-S-177 D2, Puck: PSL-0509, Cryo: direct from soaking solution	Resolution 1.63 Å R-free 0.171
9OB9 Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with with ADP and CTP Deposited 2025-04-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Not recorded	CTP CYTIDINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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 ADP and CTP, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. Partial ADP and CTP occupancy at same sites. plate Liu-S-177 D2, Puck: PSL-0514, Cryo: direct from soaking solution	Resolution 1.60 Å R-free 0.178
9OBA Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum containing phosphorylated active site histidine Deposited 2025-04-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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 ADP and CTP, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. Crystals were soaked with 10mM ATP for 4 hours which phosphorylated His139. No ADP bound after phosphorylation. plate Liu-S-177 D2, Puck: PSL-0411, Cryo: direct	Resolution 1.58 Å R-free 0.168
9OBC Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with with ADP Deposited 2025-04-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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 ADP, 5mM MgCl2 in 40% MPD, 0.1M sodium Formate, 0.1M Citrate pH 5.5. plate Liu-S-177 D2, Puck: PSL-0511, Cryo: direct from soaking solution	Resolution 1.62 Å R-free 0.180
9OD6 Crystal structure of nucleoside-diphosphate kinase from Cryptosporidium parvum in complex with citrate Deposited 2025-04-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Not recorded	CIT CITRIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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	Resolution 1.45 Å R-free 0.168
9PG0 Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum in complex with AMP Deposited 2025-07-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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	Resolution 1.45 Å R-free 0.155
9YN9 Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum (GMP complex) Deposited 2025-10-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa）	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 6 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Index C6: 1.5 M ammonium sulfate, 100 mM Bis-Tris pH 6.5, 100mM NaCl, CrpaA.01302.a.B2.PW39348 at 9.2 mg/mL. overnight soak in 2mM GMP in crystallant, Liu-S-177 H4 , Puck: PSL-0103, Cryo: 2.5M ammonium sulfate.	Resolution 1.64 Å R-free 0.176
9ZOG Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum (Apo, hexamer) Deposited 2025-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 26–173（148 aa） Chain B 26–173（148 aa） Chain C 26–173（148 aa） Chain D 26–173（148 aa） Chain E 26–173（148 aa） Chain F 26–173（148 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 10 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Berkeley H10: 100 mM Bis-Tris pH 6.5; 200 mM Sodium acetate, 25% PEG 4000. CrpaA.01302.a.B2.PW39348 at 18.8 mg/mL. Screened as ButhA.01370.b.B2 but contaminating CrpaA.01302.a.B2 on the column from a preceding purification is what crystallized. plate 20365 H10 drop 2, Puck: PSL-1602, Cryo: 20% ethylene + 80% crystallant	Resolution 1.48 Å R-free 0.161

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5CR64_CRYPI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–156； UniProt 26–173 Author chain B； PDBConstruct 9–156； UniProt 26–173 Author chain C； PDBConstruct 9–156； UniProt 26–173

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pfy
Deposition date deposition_date	2025-07-07
最后修订 last_revision	2025-07-16
Structure title title	Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum in complex with ATP
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, nucleoside-diphosphate kinase; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.98 Å
Radius of gyration Rg (electron density) rg_electron	24.44 Å
Forward intensity I(0) i0	41395100.00
Molecular weight molecular_weight	50076.0 kDa
Excluded volume excluded_volume	62916 Å³
Envelope volume envelope_volume	75431 Å³
Hydration-shell volume shell_volume	25615 Å³
Envelope diameter envelope_diameter	79.7 Å
Shell Rg shell_rg	31.71 Å
Envelope Rg envelope_rg	24.64 Å
Shape Rg shape_rg	24.45 Å
Total Rg total_rg	25.23 Å
Total atoms total_atoms	3509
Residues n_residues	444
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	79.0 Å
Rg (real space) rg_real	24.92 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	4.1400e+07
I(0) uncertainty (real space) i0_real_error	4.9760e+05
Rg (reciprocal space) rg_reciprocal	24.93 Å
I(0) (reciprocal space) i0_reciprocal	41400000.0000
Solution quality estimate total_estimate	0.9066
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.207
Kurtosis Kurtosis kurtosis	-0.658
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19390000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	nucleoside-diphosphate kinase
Molecular weight formula_weight	17692.3 kDa
EC 编号 ec_number	2.7.4.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4119

MAHHHHHHVEQTYLMIKPDGIQRQVVGEIISRFEKRGYRIAAMKLTIATPAILEEHYAEHKGKPFLPGLIEKMTGPVLCMVFEGVDVIAQARKMMGSTRPGEAAPGTIRADFCQQAGRNLIHGSDSAESAKREISLWFKPEEIQSYKLALSDYIFE

来源 Source

来源生物 organism	Cryptosporidium parvum Iowa II
NCBI Class编号 ncbi_taxonomy_id	353152
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	451

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8. Citations (1)

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Unit-cell length a length_a	69.815 Å
Unit-cell length b length_b	69.815 Å
Unit-cell length c length_c	315.861 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.420 Å
Low-resolution limit resolution_low	48.010 Å
R factor r_factor	0.1284
R_work r_work	0.1270
R_free r_free	0.1558

fit	/app/data/saxs_computation/pf/9pfy/9pfy.fit
pddf	/app/data/pr_computation/pf/9pfy/9pfy.pr.out
profile	/app/data/saxs_computation/pf/9pfy/9pfy.dat

Crystal structure of nucleoside-diphosphate kinase Cryptosporidium parvum in complex with ATP

1. Protein Identity and Related Structures Protein Identity & Related Structures

nucleoside-diphosphate kinase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction