SAXSdb — 3fvd

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

Mandelate racemase/muconate lactonizing enzyme

Roseovarius nubinhibens ISM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	MAGNESIUM ION × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3SNF7_9RHOB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–370； UniProt 2–368 Author chain B； PDBConstruct 4–370； UniProt 2–368

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	3fvd
Deposition date deposition_date	2009-01-15
Structure title title	Crystal structure of a member of enolase superfamily from ROSEOVARIUS NUBINHIBENS ISM complexed with magnesium
Keywords keywords	STRUCTURAL GENOMICS, HYDROLASE, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC; HYDROLASE
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.

3fvd__assembly_1__model_1

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

Download this curve (.dat)

3fvd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fvd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.87 Å
Rg (electron density)	40.22 Å
Total Rg	40.59 Å
Atom count	21956
Residues	2912
Excluded volume	386800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fvd__assembly_1__model_1`	octameric （8）	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	Mandelate racemase/muconate lactonizing enzyme
Molecular weight formula_weight	40676.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	5859

MSLRITRLTVFHLDLPLAKPYWLSGGRLKFDRLDSTYLRIDTDEGVTGWGEGCPWGHSYLPAHGPGLRAGIATLAPHLLGLDPRSLDHVNRVMDLQLPGHSYVKSPIDMACWDILGQVAGLPLWQLLGGEAATPVPINSSISTGTPDQMLGLIAEAAAQGYRTHSAKIGGSDPAQDIARIEAISAGLPDGHRVTFDVNRAWTPAIAVEVLNSVRARDWIEQPCQTLDQCAHVARRVANPIMLDECLHEFSDHLAAWSRGACEGVKIKPNRVGGLTRARQIRDFGVSVGWQMHIEDVGGTALADTAALHLAASTPEANRLASWLGHAHLADDPIPGQGARNRDGLATPPSAPGLGVIPDPEALGRPVASYDEGHHHHHH

Source Source

Source organism organism	Roseovarius nubinhibens ISM
NCBI taxonomy ID ncbi_taxonomy_id	89187
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	342

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3fvda1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.0 — automated matches

Domain ID domain_id	d3fvda2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.0 — automated matches

Domain ID domain_id	d3fvda3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3fvda4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3fvdb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.54 — Enolase N-terminal domain-like
Superfamily Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
Family Family family	d.54.1.0 — automated matches

Domain ID domain_id	d3fvdb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.11 — Enolase C-terminal domain-like
Family Family family	c.1.11.0 — automated matches

Domain ID domain_id	d3fvdb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3fvdb4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3fvdA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	3fvdA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

Domain ID domain_id	3fvdB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	3fvdB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

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Unit-cell length a length_a	126.518 Å
Unit-cell length b length_b	126.518 Å
Unit-cell length c length_c	97.294 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	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1670
R_work r_work	0.1640
R_free r_free	0.2250

Crystal structure of a member of enolase superfamily from ROSEOVARIUS NUBINHIBENS ISM complexed with magnesium

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

Mandelate racemase/muconate lactonizing enzyme

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

3fvd__assembly_1__model_1

3fvd__assembly_1__model_1 | I(q)

3fvd__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a member of enolase superfamily from ROSEOVARIUS NUBINHIBENS ISM complexed with magnesium

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

Mandelate racemase/muconate lactonizing enzyme

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

3fvd__assembly_1__model_1

3fvd__assembly_1__model_1 | I(q)

3fvd__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)