SAXSdb — 1odh

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

MGCM1

MUS MUSCULUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;5'-D(CPGPAPTPGPCPGPGPGPTP GPCPA)-3' ; × 1 ;5'-D(TPGPCPAPCPCPCPGPCPAP TPCPG)-3' ; × 1 ZINC ION × 2 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P70348
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–174； UniProt 1–174

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	1odh
Deposition date deposition_date	2003-02-19
Structure title title	Structure of the GCM domain bound to DNA
Keywords keywords	TRANSCRIPTION FACTOR/DNA, TRANSCRIPTION FACTOR, DNA-BINDING DOMAIN, PROTEIN-DNA COMPLEX, TRANSCRIPTION FACTOR-DNA complex; TRANSCRIPTION FACTOR/DNA
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.

1odh__assembly_1__model_1

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

Download this curve (.dat)

1odh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1odh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.14 Å
Rg (electron density)	18.33 Å
Total Rg	19.24 Å
Atom count	1806
Residues	184
Excluded volume	30001 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1odh__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	MGCM1
Molecular weight formula_weight	20463.2 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	1810

MELDDFDPEDKEILSWDINDVKLPQNVKTTDWFQEWPDSYVKHIYSSDDRNAQRHLSSWAMRNTNNHNSRILKKSCLGVVVCSRDCSTEEGRKIYLRPAICDKARQKQQRKSCPNCNGPLKLIPCRGHGGFPVTNFWRHDGRFIFFQSKGEHDHPRPETKLEAEARRAMKKVHM

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	;5'-D(CPGPAPTPGPCPGPGPGPTP GPCP*A)-3' ;
Molecular weight formula_weight	4032.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CGATGCGGGTGCA

Entity 3 Entity 3 polymer

Description description	;5'-D(TPGPCPAPCPCPCPGPCPAP TPCP*G)-3' ;
Molecular weight formula_weight	3912.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TGCACCCGCATCG

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1odha_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.239 — GCM domain
Superfamily Superfamily superfamily	d.239.1 — GCM domain
Family Family family	d.239.1.1 — GCM domain

CATH v4.4 (2 domains)

Domain ID domain_id	1odhA01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	670 — GCM domain, large subdomain

Domain ID domain_id	1odhA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3530 — GCM motif

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Unit-cell length a length_a	41.810 Å
Unit-cell length b length_b	52.910 Å
Unit-cell length c length_c	62.970 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	19.350 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2810

Structure of the GCM domain bound to DNA

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

MGCM1

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

1odh__assembly_1__model_1

1odh__assembly_1__model_1 | I(q)

1odh__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the GCM domain bound to DNA

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

MGCM1

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

1odh__assembly_1__model_1

1odh__assembly_1__model_1 | I(q)

1odh__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)