SAXSdb — 9x6i

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

SDR family NAD(P)-dependent oxidoreductase

Paracoccus litorisediminis

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–244 Chain B； UniProt 2–244 Chain E； UniProt 2–244 Chain F； UniProt 2–244	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 11 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.90 Å R-free 0.199
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 2–244 Chain G； UniProt 2–244 Chain I； UniProt 2–244 Chain J； UniProt 2–244	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.90 Å R-free 0.199
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 2–244 Chain H； UniProt 2–244 Chain K； UniProt 2–244 Chain L； UniProt 2–244	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；293 K；0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.90 Å R-free 0.199

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 9X6I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XAX Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (NADP+ and tartronate bound form) Deposited 2025-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–244（243 aa） Chain F 2–244（243 aa） Chain I 2–244（243 aa） Chain J 2–244（243 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 TTN TARTRONATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；25% w/v PEG 3350, 0.1M Tris pH 8.5	Resolution 2.08 Å R-free 0.201
9XAX Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (NADP+ and tartronate bound form) Deposited 2025-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain B 2–244（243 aa） Chain E 2–244（243 aa） Chain G 2–244（243 aa） Chain K 2–244（243 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 TTN TARTRONATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；25% w/v PEG 3350, 0.1M Tris pH 8.5	Resolution 2.08 Å R-free 0.201
9XAX Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (NADP+ and tartronate bound form) Deposited 2025-10-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 2–244（243 aa） Chain D 2–244（243 aa） Chain H 2–244（243 aa） Chain L 2–244（243 aa）	Not recorded	NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 TTN TARTRONATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；25% w/v PEG 3350, 0.1M Tris pH 8.5	Resolution 2.08 Å R-free 0.201

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A844HLS7_9RHOB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–255； UniProt 2–244 Author chain B； PDBConstruct 13–255； UniProt 2–244 Author chain C； PDBConstruct 13–255； UniProt 2–244 Author chain D； PDBConstruct 13–255； UniProt 2–244 Author chain E； PDBConstruct 13–255； UniProt 2–244 Author chain F； PDBConstruct 13–255； UniProt 2–244 Author chain G； PDBConstruct 13–255； UniProt 2–244 Author chain H； PDBConstruct 13–255； UniProt 2–244 Author chain I； PDBConstruct 13–255； UniProt 2–244 Author chain J； PDBConstruct 13–255； UniProt 2–244 Author chain K； PDBConstruct 13–255； UniProt 2–244 Author chain L； PDBConstruct 13–255； UniProt 2–244

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	9x6i
Deposition date deposition_date	2025-10-15
Structure title title	Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (ligand-free form)
Keywords keywords	short chain dehydrogenase /reductase superfamily, OXIDOREDUCTASE; OXIDOREDUCTASE
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	50.06 Å
Radius of gyration Rg (electron density) rg_electron	49.96 Å
Forward intensity I(0) i0	1366500000.00
Molecular weight molecular_weight	298190.0 kDa
Excluded volume excluded_volume	369550 Å³
Envelope volume envelope_volume	521220 Å³
Hydration-shell volume shell_volume	87127 Å³
Envelope diameter envelope_diameter	169.1 Å
Shell Rg shell_rg	52.82 Å
Envelope Rg envelope_rg	49.69 Å
Shape Rg shape_rg	49.97 Å
Total Rg total_rg	49.99 Å
Total atoms total_atoms	20902
Residues n_residues	2852
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	165.4 Å
Rg (real space) rg_real	50.08 Å
Rg uncertainty (real space) rg_real_error	1.92 Å
I(0) (real space) i0_real	1.3670e+09
I(0) uncertainty (real space) i0_real_error	2.9460e+07
Rg (reciprocal space) rg_reciprocal	50.03 Å
I(0) (reciprocal space) i0_reciprocal	1366000000.0000
Solution quality estimate total_estimate	0.8677
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	58.7 Å
Skewness Skewness skewness	0.353
Kurtosis Kurtosis kurtosis	-0.400
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	84520000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.665

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SDR family NAD(P)-dependent oxidoreductase
Molecular weight formula_weight	27366.1 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	22752

MRGSHHHHHHGSKNILITGGGSGVGRATARRFLIEGWQVGLIGRREDALQETAEDNPNALILPCDVTDEAAVDATFAKVASSWGRLDILFNNAGAVLPSTLIDEITVADWRRVTDVNITGMFLCARAAFRQMRNQQPMGGRIINNGSISADVPRPGSVPYTVSKHAVTGLTRTLSLDGRPFNIACGQVDIGNALTDMAVAMTKGVPQADGSTKIEPVIDVKTVADSVWHMATMPEGANIQWLTVMATNMPYIGRG

来源 Source

来源生物 organism	Paracoccus litorisediminis
NCBI Class编号 ncbi_taxonomy_id	2006130
宿主生物 host_organism	Escherichia coli DH5[alpha]

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	12

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1826

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8. Citations (1)

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Unit-cell length a length_a	69.763 Å
Unit-cell length b length_b	73.454 Å
Unit-cell length c length_c	141.288 Å
Unit-cell angle α angle_alpha	83.15 °
Unit-cell angle β angle_beta	80.76 °
Unit-cell angle γ angle_gamma	83.81 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	47.740 Å
R factor r_factor	0.1701
R_work r_work	0.1685
R_free r_free	0.1993

fit	/app/data/saxs_computation/x6/9x6i/9x6i.fit
pddf	/app/data/pr_computation/x6/9x6i/9x6i.pr.out
profile	/app/data/saxs_computation/x6/9x6i/9x6i.dat

Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (ligand-free form)

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

SDR family NAD(P)-dependent oxidoreductase

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