SAXSdb — 1d2m

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

EXCINUCLEASE ABC SUBUNIT B

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	octyl beta-D-glucopyranoside × 3 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UVRB_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–665； UniProt 1–665

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	1d2m
Deposition date deposition_date	1999-09-25
Structure title title	UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME
Keywords keywords	MULTIDOMAIN PROTEIN, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, HYDROLASE; 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.

1d2m__assembly_1__model_1

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

Download this curve (.dat)

1d2m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1d2m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.20 Å
Rg (electron density)	27.40 Å
Total Rg	28.25 Å
Atom count	4524
Residues	552
Excluded volume	80889 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1d2m__assembly_1__model_1`	monomeric （1）	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	EXCINUCLEASE ABC SUBUNIT B
Molecular weight formula_weight	76266.1 kDa
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	4859

MTFRYRGPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNKILAAQLAAEFRELFPENAVEYFISYYDYYQPEAYVPGKDLYIEKDASINPEIERLRHSTTRSLLTRRDVIVVASVSAIYGLGDPREYRARNLVVERGKPYPREVLLERLLELGYQRNDIDLSPGRFRAKGEVLEIFPAYETEPIRVELFGDEVERISQVHPVTGERLRELPGFVLFPATHYLSPEGLEEILKEIEKELWERVRYFEERGEVLYAQRLKERTLYDLEMLRVMGTCPGVENYARYFTGKAPGEPPYTLLDYFPEDFLVFLDESHVTVPQLQGMYRGDYARKKTLVDYGFRLPSALDNRPLRFEEFLERVSQVVFVSATPGPFELAHSGRVVEQIIRPTGLLDPLVRVKPTENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQRAIEETNRRRALQEAYNLEHGITPETVRKEVRAVIRPEGYEEAPLEADLSGEDLRERIAELELAMWQAAEALDFERAARLRDEIRALEARLQGVRAPEPVPGGRKRKRR

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	335

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d2ma1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d1d2ma2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

CATH v4.4 (4 domains)

Domain ID domain_id	1d2mA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1d2mA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2060 — Penicillin-binding protein 1b fold
Homologous superfamily homologous superfamily	10 — Penicillin-binding protein 1b domain

Domain ID domain_id	1d2mA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	1d2mA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	135.040 Å
Unit-cell length b length_b	135.040 Å
Unit-cell length c length_c	106.756 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2530

UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME

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

EXCINUCLEASE ABC SUBUNIT B

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

1d2m__assembly_1__model_1

1d2m__assembly_1__model_1 | I(q)

1d2m__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

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)

UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME

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

EXCINUCLEASE ABC SUBUNIT B

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

1d2m__assembly_1__model_1

1d2m__assembly_1__model_1 | I(q)

1d2m__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

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)