SAXSdb — 5k87

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

2-methyl-aconitate isomerase

Shewanella oneidensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MALONATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRPF_SHEON
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–399； UniProt 2–397 Author chain B； PDBConstruct 4–399； UniProt 2–397

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	5k87
Deposition date deposition_date	2016-05-27
Structure title title	crystal structure of malonate bound to methylaconitate isomerase PrpF from Shewanella oneidensis
Keywords keywords	PrpF methylaconitate isomerase 2-MMC, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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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.

5k87__assembly_1__model_1

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

Download this curve (.dat)

5k87__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5k87__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.86 Å
Rg (electron density)	27.02 Å
Total Rg	27.80 Å
Atom count	5724
Residues	775
Excluded volume	101960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5k87__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	2-methyl-aconitate isomerase
Molecular weight formula_weight	41786.3 kDa
EC 编号 ec_number	5.3.3.-
Mutation mutation	K73E
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	7024

GASSNKLFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGATSSTSETVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAADDDGEGGCMFPTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPKP

Source Source

Source organism organism	Shewanella oneidensis
NCBI taxonomy ID ncbi_taxonomy_id	211586
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1113

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5k87a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.0 — automated matches

Domain ID domain_id	d5k87a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.0 — automated matches

Domain ID domain_id	d5k87b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.0 — automated matches

Domain ID domain_id	d5k87b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5k87A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	5k87A02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	5k87B01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	5k87B02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

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Unit-cell length a length_a	51.825 Å
Unit-cell length b length_b	103.393 Å
Unit-cell length c length_c	78.088 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.219 Å
Low-resolution limit resolution_low	31.360 Å
R factor r_factor	0.1638
R_work r_work	0.1628
R_free r_free	0.1819

crystal structure of malonate bound to methylaconitate isomerase PrpF from Shewanella oneidensis

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

2-methyl-aconitate isomerase

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

5k87__assembly_1__model_1

5k87__assembly_1__model_1 | I(q)

5k87__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

crystal structure of malonate bound to methylaconitate isomerase PrpF from Shewanella oneidensis

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

2-methyl-aconitate isomerase

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

5k87__assembly_1__model_1

5k87__assembly_1__model_1 | I(q)

5k87__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)