SAXSdb — 3req

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

METHYLMALONYL-COA MUTASE

Propionibacterium freudenreichii subsp. shermanii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	METHYLMALONYL-COA MUTASE × 1 （P11652） COBALAMIN × 1 ADENOSINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MUTB_PROFR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–727； UniProt 1–727

METHYLMALONYL-COA MUTASE

Propionibacterium freudenreichii subsp. shermanii

UniProt P11652

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	METHYLMALONYL-COA MUTASE × 1 （P11653） COBALAMIN × 1 ADENOSINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MUTA_PROFR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–637； UniProt 1–637

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	3req
Deposition date deposition_date	1997-12-04
Structure title title	METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)
Keywords keywords	COMPLEX (ISOMERASE-DEOXYADENOSINE), ISOMERASE, MUTASE, INTRAMOLECULAR TRANSFERASE, COMPLEX (ISOMERASE-DEOXYADENOSINE) complex; COMPLEX (ISOMERASE/DEOXYADENOSINE)
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.

3req__assembly_1__model_1

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

Download this curve (.dat)

3req__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3req__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.07 Å
Rg (electron density)	33.33 Å
Total Rg	33.89 Å
Atom count	10285
Residues	1345
Excluded volume	182230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3req__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 (4)

Entity 1 Entity 1 polymer

Description description	METHYLMALONYL-COA MUTASE
Molecular weight formula_weight	80137.9 kDa
EC 编号 ec_number	5.4.99.2
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	10285

STLPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASLDA

Source Source

Source organism organism	Propionibacterium freudenreichii subsp. shermanii
NCBI taxonomy ID ncbi_taxonomy_id	1752
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	METHYLMALONYL-COA MUTASE
Molecular weight formula_weight	69430.2 kDa
EC 编号 ec_number	5.4.99.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKRLTVHTVDGIDIVPMYRPKDAPKKLGYPGVAPFTRGTTVRNGDMDAWDVRALHEDPDEKFTRKAILEGLERGVTSLLLRVDPDAIAPEHLDEVLSDVLLEMTKVEVFSRYDQGAAAEALVSVYERSDKPAKDLALNLGLDPIGFAALQGTEPDLTVLGDWVRRLAKFSPDSRAVTIDANIYHNAGAGDVAELAWALATGAEYVRALVEQGFTATEAFDTINFRVTATHDQFLTIARLRALREAWARIGEVFGVDEDKRGARQNAITSWRELTREDPYVNILRGSIATFSASVGGAESITTLPFTQALGLPEDDFPLRIARNTGIVLAEEVNIGRVNDPAGGSYYVESLTRSLADAAWKEFQEVEKLGGMSKAVMTEHVTKVLDACNAERAKRLANRKQPITAVSEFPMIGARSIETKPFPAAPARKGLAWHRDSEVFEQLMDRSTSVSERPKVFLACLGTRRDFGGREGFSSPVWHIAGIDTPQVEGGTTAEIVEAFKKSGAQVADLCSSAKVYAQQGLEVAKALKAAGAKALYLSGAFKEFGDDAAEAEKLIDGRLFMGMDVVDTLSSTLDILGVAK

Source Source

Source organism organism	Propionibacterium freudenreichii subsp. shermanii
NCBI taxonomy ID ncbi_taxonomy_id	1752
Host organism host_organism	K38 PGP1-2

Entity 3 Entity 3 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE
Molecular weight formula_weight	267.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3reqa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

Domain ID domain_id	d3reqa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
Family Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

Domain ID domain_id	d3reqb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.1 — Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain

Domain ID domain_id	d3reqb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.6 — Cobalamin (vitamin B12)-binding domain
Family Family family	c.23.6.1 — Cobalamin (vitamin B12)-binding domain

CATH v4.4 (4 domains)

Domain ID domain_id	3reqA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

Domain ID domain_id	3reqA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	280 — Cobalamin-binding domain

Domain ID domain_id	3reqB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	240 — Methylmalonyl-CoA mutase

Domain ID domain_id	3reqB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	280 — Cobalamin-binding domain

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Unit-cell length a length_a	110.910 Å
Unit-cell length b length_b	110.910 Å
Unit-cell length c length_c	257.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.3130
R_free r_free	0.3930

METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)

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

METHYLMALONYL-COA MUTASE

State in the Current Structure

Other States of the Same Protein in the Database

METHYLMALONYL-COA MUTASE

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

3req__assembly_1__model_1

3req__assembly_1__model_1 | I(q)

3req__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)

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

METHYLMALONYL-COA MUTASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

METHYLMALONYL-COA MUTASE

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

3req__assembly_1__model_1

3req__assembly_1__model_1 | I(q)

3req__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)