SAXSdb — 7nnk

▼

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

HpcH/HpaI aldolase

Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	3-HYDROXYPYRUVIC ACID × 3 MAGNESIUM ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5VH82_SPHWW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–252； UniProt 2–251 Author chain B； PDBConstruct 3–252； UniProt 2–251

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	7nnk
Deposition date deposition_date	2021-02-25
Structure title title	Crystal structure of S116A mutant of hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate
Keywords keywords	Class II Pyruvate Aldolase, Metal Dependent, Aldol Reaction, Hydroxypyruvate, Pyruvate, Aldolase, Class II, LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7nnk__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7nnk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7nnk__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.11 Å
Rg (electron density)	31.65 Å
Total Rg	32.30 Å
Atom count	22440
Residues	1497
Excluded volume	199090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7nnk__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	HpcH/HpaI aldolase
Molecular weight formula_weight	26768.5 kDa
Mutation mutation	S116A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7915

HHNKVRTCWNEGRPALAGWLQLPGTLHAEALARLDYDAVVIDMQHSPIDFGQVAPMLIAIELGGAEPFVRTQVNDPSDIMKLLDAGAYGIIAPMVNTRAEAQTLASALHYSPRGLRAFGPRRPSLRYGSGYLAQASETVVGLAMIETREALANIDEILSVDGIDGVFIGPTDLALDLGHAPLVDTEEAEVVSAIAHVRERAHAAGKRVGIFCGSGGFARVKLAEGFDFVTAAPDLAMLSAAARQVIADARAL

Source Source

Source organism organism	Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
NCBI taxonomy ID ncbi_taxonomy_id	392499
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	3-HYDROXYPYRUVIC ACID
Molecular weight formula_weight	104.1 kDa
Source method src_method	syn
Copy count entity_count	1

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	299

▶

Unit-cell length a length_a	71.327 Å
Unit-cell length b length_b	71.327 Å
Unit-cell length c length_c	223.185 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	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	59.533 Å
R factor r_factor	—
R_work r_work	0.1831
R_free r_free	0.2247

Crystal structure of S116A mutant of hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate

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

HpcH/HpaI aldolase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7nnk__assembly_1__model_1

7nnk__assembly_1__model_1 | I(q)

7nnk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of S116A mutant of hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate

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

HpcH/HpaI aldolase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7nnk__assembly_1__model_1

7nnk__assembly_1__model_1 | I(q)

7nnk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)