1vdh

Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8

Method: X-RAY DIFFRACTION

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

muconolactone isomerase-like protein

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1714_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–249； UniProt 1–249 Author chain B； PDBConstruct 1–249； UniProt 1–249 Author chain C； PDBConstruct 1–249； UniProt 1–249 Author chain D； PDBConstruct 1–249； UniProt 1–249 Author chain E； PDBConstruct 1–249； UniProt 1–249

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	1vdh
Deposition date deposition_date	2004-03-22
Structure title title	Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8
Keywords keywords	beta barrel, STRUCTURAL GENOMICS, RIKEN Structural Genomics/Proteomics Initiative, RSGI, UNKNOWN FUNCTION; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1vdh__assembly_1__model_1

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

Download this curve (.dat)

1vdh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vdh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.05 Å
Rg (electron density)	30.74 Å
Total Rg	31.73 Å
Atom count	10150
Residues	1235
Excluded volume	179730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vdh__assembly_1__model_1`	pentameric （5）	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 (2)

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1vdha_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.10 — Chlorite dismutase-like

Domain ID domain_id	d1vdhb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.10 — Chlorite dismutase-like

Domain ID domain_id	d1vdhc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.10 — Chlorite dismutase-like

Domain ID domain_id	d1vdhd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.10 — Chlorite dismutase-like

Domain ID domain_id	d1vdhe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.10 — Chlorite dismutase-like

CATH v4.4 (10 domains)

Domain ID domain_id	1vdhA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	1vdhA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	1vdhB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	1vdhB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	1vdhC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	1vdhC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	1vdhD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	1vdhD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	1vdhE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	1vdhE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

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Unit-cell length a length_a	99.738 Å
Unit-cell length b length_b	123.136 Å
Unit-cell length c length_c	131.439 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	20

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.2180

Description description	muconolactone isomerase-like protein
Molecular weight formula_weight	28944.8 kDa
Mutation mutation	K182E
Source method src_method	man
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	11168

Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8

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

muconolactone isomerase-like protein

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

1vdh__assembly_1__model_1

1vdh__assembly_1__model_1 | I(q)

1vdh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1018

Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8

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

muconolactone isomerase-like protein

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

1vdh__assembly_1__model_1

1vdh__assembly_1__model_1 | I(q)

1vdh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

CATH v4.4 (10 domains)

7. Citations (1)