1a7j

PHOSPHORIBULOKINASE FROM RHODOBACTER SPHEROIDES

Method: X-RAY DIFFRACTION Dmax: 62.6 Å Quality: EXCELLENT

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

PHOSPHORIBULOKINASE

Rhodobacter sphaeroides

UniProt P12033

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–290 Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5;PROTEIN WAS CRYSTALLIZED FROM AMMONIUM PHOSPHATE, pH 5.0 Resolution 2.50 Å R-free 0.284
2 Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 1–290 Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5;PROTEIN WAS CRYSTALLIZED FROM AMMONIUM PHOSPHATE, pH 5.0 Resolution 2.50 Å R-free 0.284
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–290 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5;PROTEIN WAS CRYSTALLIZED FROM AMMONIUM PHOSPHATE, pH 5.0 Resolution 2.50 Å R-free 0.284

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name KPPR1_RHOSH
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–290; UniProt 1–290

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1a7j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1a7j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1a7j
Deposition date deposition_date1998-03-16
Structure title titlePHOSPHORIBULOKINASE FROM RHODOBACTER SPHEROIDES
Keywords keywordsTRANSFERASE, KINASE, CALVIN CYCLE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.51
Radius of gyration Rg (electron density) rg_electron19.27
Forward intensity I(0) i017456200.00
Molecular weight molecular_weight31044.0 kDa
Excluded volume excluded_volume38679 ų
Envelope volume envelope_volume47098 ų
Hydration-shell volume shell_volume20348 ų
Envelope diameter envelope_diameter63.4
Shell Rg shell_rg25.70
Envelope Rg envelope_rg19.38
Shape Rg shape_rg19.27
Total Rg total_rg20.21
Total atoms total_atoms2192
Residues n_residues279
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax62.6
Rg (real space) rg_real20.40
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real1.7460e+07
I(0) uncertainty (real space) i0_real_error2.3240e+05
Rg (reciprocal space) rg_reciprocal20.42
I(0) (reciprocal space) i0_reciprocal17460000.0000
Solution quality estimate total_estimate0.9096
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9
Skewness Skewness skewness0.145
Kurtosis Kurtosis kurtosis-0.487
Angular range angular_range— – 0.3900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3042000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1a7ja_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.6 — Phosphoribulokinase/pantothenate kinase

CATH v4.4 (1 domains)

Domain ID domain_id1a7jA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (2)

9. Files and Curves (10)