SAXSdb — 5edf

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

FrpC operon protein

Neisseria meningitidis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	HEXAETHYLENE GLYCOL × 1 PENTAETHYLENE GLYCOL × 1 SODIUM ION × 1 AZIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q08840_NEIME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–229； UniProt 43–271

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	5edf
Deposition date deposition_date	2015-10-21
Structure title title	Crystal structure of the selenomethionine-substituted iron-regulated protein FrpD from Neisseria meningitidis
Keywords keywords	Selenomethionine-substituted iron-regulated protein FrpD, FrpC-binding protein, novel fold, metal transport, unknown function; 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.

5edf__assembly_1__model_1

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

Download this curve (.dat)

5edf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5edf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.32 Å
Rg (electron density)	19.16 Å
Total Rg	20.11 Å
Atom count	1888
Residues	220
Excluded volume	33365 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5edf__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 (6)

Entity 1 Entity 1 polymer

Description description	FrpC operon protein
Molecular weight formula_weight	28896.3 kDa
Mutation mutation	54:MSE; 70:MSE; 156:MSE; 168:MSE
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	2217

KEQTSFNNPEPMTGFEHTVTFDFQGTKMVIPYGYLARYTQDNATKWLSDTPGQDAYSINLIEISVYYKKTDQGWVLEPYNQQNKAHFIQFLRDGLDSVDDIVIRKDACSLSTTMGERLLTYGVKKMPSAYPEYEAYEDKRHIPENPYFHEFYYIKKGENPAIITHRNNRINQTEEDSYSTSVGSCINGFTVQYYPFIREKQQLTQQELVGYHQQVEQLVQSFVNNSNKKENLYFQGLEHHHHHH

Source Source

Source organism organism	Neisseria meningitidis
NCBI taxonomy ID ncbi_taxonomy_id	487
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	274

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Unit-cell length a length_a	38.293 Å
Unit-cell length b length_b	38.829 Å
Unit-cell length c length_c	165.670 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	4

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	25.200 Å
R factor r_factor	0.1690
R_work r_work	0.1678
R_free r_free	0.1927

Crystal structure of the selenomethionine-substituted iron-regulated protein FrpD from Neisseria meningitidis

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

FrpC operon 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

5edf__assembly_1__model_1

5edf__assembly_1__model_1 | I(q)

5edf__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (2)

Crystal structure of the selenomethionine-substituted iron-regulated protein FrpD from Neisseria meningitidis

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

FrpC operon 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

5edf__assembly_1__model_1

5edf__assembly_1__model_1 | I(q)

5edf__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (2)