2p5v

Crystal Structure of Transcriptional Regulator NMB0573 from Neisseria Meningitidis

Method: X-RAY DIFFRACTION

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

Transcriptional regulator, LRP/AsnC family

Neisseria meningitidis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	CALCIUM ION × 8 CHLORIDE ION × 10 GLYCEROL × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9K0L9_NEIMB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–162； UniProt 28–187 Author chain B； PDBConstruct 3–162； UniProt 28–187 Author chain C； PDBConstruct 3–162； UniProt 28–187 Author chain D； PDBConstruct 3–162； UniProt 28–187 Author chain E； PDBConstruct 3–162； UniProt 28–187 Author chain F； PDBConstruct 3–162； UniProt 28–187 Author chain G； PDBConstruct 3–162； UniProt 28–187 Author chain H； PDBConstruct 3–162； UniProt 28–187

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	2p5v
Deposition date deposition_date	2007-03-16
Structure title title	Crystal Structure of Transcriptional Regulator NMB0573 from Neisseria Meningitidis
Keywords keywords	;NMB0573, Transcriptional regulator, Lrp/AsnC-family, Structural Genomics, Structural and functional analysis of N. meninigitidis transcriptional regulators, Oxford Protein Production Facility, OPPF, 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.

2p5v__assembly_1__model_1

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

Download this curve (.dat)

2p5v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2p5v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.00 Å
Rg (electron density)	35.70 Å
Total Rg	36.19 Å
Atom count	9910
Residues	1235
Excluded volume	178150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2p5v__assembly_1__model_1`	octameric （8）	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	Transcriptional regulator, LRP/AsnC family
Molecular weight formula_weight	18288.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	10670

GPMPQLTLDKTDIKILQVLQENGRLTNVELSERVALSPSPCLRRLKQLEDAGIVRQYAALLSPESVNLGLQAFIRVSIRKAKDAREDFAASVRKWPEVLSCFALTGETDYLLQAFFTDMNAFSHFVLDTLLSHHGVQDAQSSFVLKEIKHTTSLPLNHLLKE

Source Source

Source organism organism	Neisseria meningitidis
NCBI taxonomy ID ncbi_taxonomy_id	122586
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	760

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d2p5va1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d2p5va2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d2p5vb1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d2p5vb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d2p5vc1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d2p5vc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d2p5vd1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d2p5vd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d2p5ve1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d2p5ve2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d2p5vf1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d2p5vf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d2p5vg1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d2p5vg2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d2p5vh1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.0 — automated matches

Domain ID domain_id	d2p5vh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

CATH v4.4 (16 domains)

Domain ID domain_id	2p5vA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2p5vA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	920 — Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain

Domain ID domain_id	2p5vB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2p5vB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	920 — Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain

Domain ID domain_id	2p5vC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2p5vC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	920 — Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain

Domain ID domain_id	2p5vD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2p5vD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	920 — Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain

Domain ID domain_id	2p5vE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2p5vE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	920 — Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain

Domain ID domain_id	2p5vF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2p5vF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	920 — Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain

Domain ID domain_id	2p5vG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2p5vG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	920 — Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain

Domain ID domain_id	2p5vH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2p5vH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	920 — Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain

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Unit-cell length a length_a	65.070 Å
Unit-cell length b length_b	148.480 Å
Unit-cell length c length_c	77.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	29.590 Å
R factor r_factor	0.1793
R_work r_work	0.1762
R_free r_free	0.2379

Crystal Structure of Transcriptional Regulator NMB0573 from Neisseria Meningitidis

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

Transcriptional regulator, LRP/AsnC family

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

2p5v__assembly_1__model_1

2p5v__assembly_1__model_1 | I(q)

2p5v__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Crystal Structure of Transcriptional Regulator NMB0573 from Neisseria Meningitidis

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

Transcriptional regulator, LRP/AsnC family

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

2p5v__assembly_1__model_1

2p5v__assembly_1__model_1 | I(q)

2p5v__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)