SAXSdb — 2nvm

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

FdxN element excision controlling factor XisI

Anabaena variabilis ATCC 29413

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3MD55_ANAVT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–126； UniProt 1–125 Author chain B； PDBConstruct 2–126； UniProt 1–125

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	2nvm
Deposition date deposition_date	2006-11-13
Structure title title	Crystal structure of fdxN element excision controlling factor XisI (YP_321976.1) from Anabaena Variabilis ATCC 29413 at 2.19 A resolution
Keywords keywords	;YP_321976.1, fdxN element excision controlling factor XisI, Structural Genomics, PSI-2, Protein Structure Initiative, Joint Center for Structural Genomics, JCSG, Structural Genomics-Unknown Function COMPLEX ;; 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.

2nvm__assembly_1__model_1

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

Download this curve (.dat)

2nvm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nvm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.80 Å
Rg (electron density)	17.94 Å
Total Rg	18.92 Å
Atom count	1754
Residues	213
Excluded volume	31407 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nvm__assembly_1__model_1`	dimeric （2）	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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2nvma1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.326 — XisI-like
Superfamily Superfamily superfamily	d.326.1 — XisI-like
Family Family family	d.326.1.1 — XisI-like

Domain ID domain_id	d2nvmb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.326 — XisI-like
Superfamily Superfamily superfamily	d.326.1 — XisI-like
Family Family family	d.326.1.1 — XisI-like

CATH v4.4 (2 domains)

Domain ID domain_id	2nvmA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	110 — XisI-like

Domain ID domain_id	2nvmB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	110 — XisI-like

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Unit-cell length a length_a	122.440 Å
Unit-cell length b length_b	122.440 Å
Unit-cell length c length_c	77.076 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	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.190 Å
Low-resolution limit resolution_low	77.152 Å
R factor r_factor	0.2030
R_work r_work	0.2010
R_free r_free	0.2440

Description description	FdxN element excision controlling factor XisI
Molecular weight formula_weight	14593.3 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	1851

Crystal structure of fdxN element excision controlling factor XisI (YP_321976.1) from Anabaena Variabilis ATCC 29413 at 2.19 A resolution

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

FdxN element excision controlling factor XisI

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

2nvm__assembly_1__model_1

2nvm__assembly_1__model_1 | I(q)

2nvm__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Anabaena variabilis ATCC 29413
NCBI taxonomy ID ncbi_taxonomy_id	240292
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

Crystal structure of fdxN element excision controlling factor XisI (YP_321976.1) from Anabaena Variabilis ATCC 29413 at 2.19 A resolution

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

FdxN element excision controlling factor XisI

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

2nvm__assembly_1__model_1

2nvm__assembly_1__model_1 | I(q)

2nvm__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)