SAXSdb — 1dik

▼

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

PYRUVATE PHOSPHATE DIKINASE

Clostridium symbiosum

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–873	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；pH 7.0	Resolution 2.30 Å

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 1DIK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GGO T453A MUTANT OF PYRUVATE, PHOSPHATE DIKINASE Deposited 2000-08-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Mutation：T453A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.294
1GGO T453A MUTANT OF PYRUVATE, PHOSPHATE DIKINASE Deposited 2000-08-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Mutation：T453A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å R-free 0.294
1JDE K22A mutant of pyruvate, phosphate dikinase Deposited 2001-06-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Mutation：K22A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；50% saturated ammonium sulfate, 100mM Hepes buffer, 100mM KCL, 0.1mM EDTA, 1mM Mercaptoethanol, 20mM imidazole buffer pH 6.5, 10mg/ml protein, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 2.80 Å
1JDE K22A mutant of pyruvate, phosphate dikinase Deposited 2001-06-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Mutation：K22A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；50% saturated ammonium sulfate, 100mM Hepes buffer, 100mM KCL, 0.1mM EDTA, 1mM Mercaptoethanol, 20mM imidazole buffer pH 6.5, 10mg/ml protein, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 2.80 Å
1KBL PYRUVATE PHOSPHATE DIKINASE Deposited 2001-11-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Not recorded	NH4 AMMONIUM ION × 2 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；50-54% saturated ammonium sulfate, 10 mg/ml protein solution in 100mM KCl and 20mM imidazole buffer (pH 6.5), 100 mM Hepes buffer (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 1.94 Å R-free 0.257
1KBL PYRUVATE PHOSPHATE DIKINASE Deposited 2001-11-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Not recorded	NH4 AMMONIUM ION × 2 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；50-54% saturated ammonium sulfate, 10 mg/ml protein solution in 100mM KCl and 20mM imidazole buffer (pH 6.5), 100 mM Hepes buffer (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 1.94 Å R-free 0.257
1KC7 Pyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate Deposited 2001-11-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Not recorded	MG MAGNESIUM ION × 2 SO4 SULFATE ION × 8 PPR PHOSPHONOPYRUVATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；54% saturated ammonium sulfate, 100mM Hepes buffer (pH 7.0), 9mg/ml protein solution consisting of: 20mM imidazole buffer (pH 6.5), 100mM KCl, 40mM phosphonopyruvate, 5mM MgCl2, 0.1mM EDTA, 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 2.20 Å R-free 0.269
1KC7 Pyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate Deposited 2001-11-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Not recorded	MG MAGNESIUM ION × 2 SO4 SULFATE ION × 8 PPR PHOSPHONOPYRUVATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；54% saturated ammonium sulfate, 100mM Hepes buffer (pH 7.0), 9mg/ml protein solution consisting of: 20mM imidazole buffer (pH 6.5), 100mM KCl, 40mM phosphonopyruvate, 5mM MgCl2, 0.1mM EDTA, 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 2.20 Å R-free 0.269
2DIK R337A MUTANT OF PYRUVATE PHOSPHATE DIKINASE Deposited 1998-09-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Mutation：R337A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；303 K；pH 7.0, temperature 303K	Resolution 2.50 Å
2DIK R337A MUTANT OF PYRUVATE PHOSPHATE DIKINASE Deposited 1998-09-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Mutation：R337A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；303 K；pH 7.0, temperature 303K	Resolution 2.50 Å
2FM4 NMR structure of the phosphoryl carrier domain of pyruvate phosphate dikinase Deposited 2006-01-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 383–510（128 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.07 M；Pressure ambient NMR sample composition 1mM Cent-I U-15N,13C; 20 mM phosphate buffer, pH 7.0, 95% H2O, 10% D2O \| 95% H2O, 10% D2O	Resolution not provided
2R82 Pyruvate phosphate dikinase (PPDK) triple mutant R219E/E271R/S262D adapts a second conformational state Deposited 2007-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–874（874 aa）	Mutation：R219E, S262D, E271R	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；50% saturated ammonium sulfate, 0.1 M Na Hepes, 28 mg/ml protein (in 20 mM imidazole (pH 6.5), 0.1 mM EDTA, 100 mM KCl, and 1mM DTT), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K	Resolution 3.60 Å R-free 0.325
9PZL Pyruvate phosphate dikinase in complex with AMP-PNP and sulfate ions Deposited 2025-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–874（874 aa） Chain B 1–874（874 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；PPDK 25mg/ml with 5mM MgCl2 + 5 mM AMPPNP in 2.3 M ammonium sulfate, 0.1 Na Hepes. Protein solution in 20 mM imidazole buffer, pH 6.5, 100 mM KCl, 0.1 mM EDTA and 1 mM mercaptoethanol	Resolution 3.00 Å R-free 0.302
9PZL Pyruvate phosphate dikinase in complex with AMP-PNP and sulfate ions Deposited 2025-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–874（874 aa） Chain D 1–874（874 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；PPDK 25mg/ml with 5mM MgCl2 + 5 mM AMPPNP in 2.3 M ammonium sulfate, 0.1 Na Hepes. Protein solution in 20 mM imidazole buffer, pH 6.5, 100 mM KCl, 0.1 mM EDTA and 1 mM mercaptoethanol	Resolution 3.00 Å R-free 0.302

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPDK_CLOSY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–874； UniProt 1–873

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dik
Deposition date deposition_date	1995-12-06
Structure title title	PYRUVATE PHOSPHATE DIKINASE
Keywords keywords	TRANSFERASE, KINASE, PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	32.05 Å
Radius of gyration Rg (electron density) rg_electron	31.94 Å
Forward intensity I(0) i0	149870000.00
Molecular weight molecular_weight	96327.0 kDa
Excluded volume excluded_volume	119920 Å³
Envelope volume envelope_volume	147580 Å³
Hydration-shell volume shell_volume	39434 Å³
Envelope diameter envelope_diameter	109.5 Å
Shell Rg shell_rg	38.13 Å
Envelope Rg envelope_rg	31.65 Å
Shape Rg shape_rg	31.95 Å
Total Rg total_rg	32.39 Å
Total atoms total_atoms	6745
Residues n_residues	869
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

▼

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

Maximum dimension Dmax dmax	107.4 Å
Rg (real space) rg_real	32.18 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.4990e+08
I(0) uncertainty (real space) i0_real_error	2.3070e+06
Rg (reciprocal space) rg_reciprocal	32.12 Å
I(0) (reciprocal space) i0_reciprocal	149900000.0000
Solution quality estimate total_estimate	0.8724
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.1 Å
Skewness Skewness skewness	0.452
Kurtosis Kurtosis kurtosis	-0.347
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22750000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.900

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PYRUVATE PHOSPHATE DIKINASE
Molecular weight formula_weight	96785.4 kDa
EC 编号 ec_number	2.7.9.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7161

MAKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSAARASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNNK

来源 Source

来源生物 organism	Clostridium symbiosum
NCBI Class编号 ncbi_taxonomy_id	1512
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	416

▼

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1dika1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.2 — Pyruvate phosphate dikinase, C-terminal domain

Domain ID domain_id	d1dika2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.1 — Phosphohistidine domain
Family Family family	c.8.1.1 — Pyruvate phosphate dikinase, central domain

Domain ID domain_id	d1dika3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.5 — Pyruvate phosphate dikinase, N-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1dikA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	1dikA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	189 — Pyruvate Phosphate di-kinase; domain 2
Homologous superfamily homologous superfamily	10 — Pyruvate Phosphate Dikinase, domain 2

Domain ID domain_id	1dikA03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphohistidine domain

Domain ID domain_id	1dikA04
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	1dikA05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1dikA06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	89.800 Å
Unit-cell length b length_b	58.800 Å
Unit-cell length c length_c	102.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	—

fit	/app/data/saxs_computation/di/1dik/1dik.fit
pddf	/app/data/pr_computation/di/1dik/1dik.pr.out
profile	/app/data/saxs_computation/di/1dik/1dik.dat

PYRUVATE PHOSPHATE DIKINASE

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

PYRUVATE PHOSPHATE DIKINASE

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)