SAXSdb — 3c8i

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

Putative membrane protein

Corynebacterium diphtheriae NCTC 13129

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6NIK4_CORDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–141； UniProt 75–215 Author chain B； PDBConstruct 1–141； UniProt 75–215

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	3c8i
Deposition date deposition_date	2008-02-12
Structure title title	Crystal structure of a putative membrane protein from Corynebacterium diphtheriae
Keywords keywords	;putative membrane protein, Corynebacterium diphtheriae, Structural genomics, PSI, MCSG, Protein Structure Initiative, Midwest Center for Structural Genomics, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
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.

3c8i__assembly_1__model_1

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

Download this curve (.dat)

3c8i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c8i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.63 Å
Rg (electron density)	24.40 Å
Total Rg	25.27 Å
Atom count	3940
Residues	512
Excluded volume	70207 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c8i__assembly_1__model_1`	tetrameric （4）	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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3c8iA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	410 — putative membrane protein from Corynebacterium diphtheriae fold
Homologous superfamily homologous superfamily	10 — putative membrane protein from Corynebacterium diphtheriae superfamily

Domain ID domain_id	3c8iB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	410 — putative membrane protein from Corynebacterium diphtheriae fold
Homologous superfamily homologous superfamily	10 — putative membrane protein from Corynebacterium diphtheriae superfamily

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Unit-cell length a length_a	50.374 Å
Unit-cell length b length_b	99.837 Å
Unit-cell length c length_c	124.621 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	62.260 Å
R factor r_factor	0.2019
R_work r_work	0.2002
R_free r_free	0.2316

Description description	Putative membrane protein
Molecular weight formula_weight	15545.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2146

Crystal structure of a putative membrane protein from Corynebacterium diphtheriae

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

Putative membrane 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

3c8i__assembly_1__model_1

3c8i__assembly_1__model_1 | I(q)

3c8i__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Corynebacterium diphtheriae NCTC 13129
NCBI taxonomy ID ncbi_taxonomy_id	257309
Host organism host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

Crystal structure of a putative membrane protein from Corynebacterium diphtheriae

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

Putative membrane 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

3c8i__assembly_1__model_1

3c8i__assembly_1__model_1 | I(q)

3c8i__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)