SAXSdb — 2nzv

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

Catabolite control protein

Bacillus megaterium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Phosphocarrier protein HPr × 2 （O69250） 1,6-di-O-phosphono-beta-D-fructofuranose × 2 SULFATE ION × 14 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCPA_BACME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 1–280； UniProt 53–332

Phosphocarrier protein HPr

Bacillus megaterium

UniProt O69250

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Catabolite control protein × 2 （P46828） 1,6-di-O-phosphono-beta-D-fructofuranose × 2 SULFATE ION × 14 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PTHP_BACME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–88； UniProt 1–88

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	2nzv
Deposition date deposition_date	2006-11-25
Structure title title	Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors G6P and FBP
Keywords keywords	CCpA, HPrser46-p, CCR, fructose-bis-phosphate, adjunct corepressor, LacI-GalR, TRANSCRIPTION; TRANSCRIPTION
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.

2nzv__assembly_1__model_1

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

Download this curve (.dat)

2nzv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nzv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.56 Å
Rg (electron density)	26.32 Å
Total Rg	27.12 Å
Atom count	5656
Residues	722
Excluded volume	100220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nzv__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 (5)

Entity 1 Entity 1 polymer

Description description	Catabolite control protein
Molecular weight formula_weight	30992.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G
Atom count atom_count	2833

RGLASKKTTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGIIFMSGNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQSLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAVEKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSVVQPMYDIGAVAMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK

Source Source

Source organism organism	Bacillus megaterium
NCBI taxonomy ID ncbi_taxonomy_id	1404
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Phosphocarrier protein HPr
Molecular weight formula_weight	9207.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MAQKTFTVTADSGIHARPATTLVQAASKFDSDINLEFNGKTVNLKSIMGVMSLGIQKGATITISAEGSDEADALAALEDTMSKEGLGE

Source Source

Source organism organism	Bacillus megaterium
NCBI taxonomy ID ncbi_taxonomy_id	1404
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	1,6-di-O-phosphono-beta-D-fructofuranose
Molecular weight formula_weight	340.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2nzvg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
Family Family family	c.93.1.1 — L-arabinose binding protein-like

Domain ID domain_id	d2nzvl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.94 — HPr-like
Superfamily Superfamily superfamily	d.94.1 — HPr-like
Family Family family	d.94.1.1 — HPr-like

CATH v4.4 (3 domains)

Domain ID domain_id	2nzvG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	2nzvG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	2nzvL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1340 — Histidine-containing Protein; Chain: A;
Homologous superfamily homologous superfamily	10 — HPr-like

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Unit-cell length a length_a	69.770 Å
Unit-cell length b length_b	69.770 Å
Unit-cell length c length_c	231.060 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	38.530 Å
R factor r_factor	0.2590
R_work r_work	0.2590
R_free r_free	0.2980

Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors G6P and FBP

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

Catabolite control protein

State in the Current Structure

Other States of the Same Protein in the Database

Phosphocarrier protein HPr

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

2nzv__assembly_1__model_1

2nzv__assembly_1__model_1 | I(q)

2nzv__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors G6P and FBP

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

Catabolite control 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

Phosphocarrier protein HPr

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

2nzv__assembly_1__model_1

2nzv__assembly_1__model_1 | I(q)

2nzv__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)