SAXSdb — 4z67

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

Coenzyme PQQ synthesis protein B

Pseudomonas putida (strain KT2440)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 D-MALATE × 2 MANGANESE (II) ION × 2 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PQQB_PSEPK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–304； UniProt 1–303

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	4z67
Deposition date deposition_date	2015-04-03
Structure title title	The 1.5-angstrom crystal structure of Mn(2+)-bound PqqB from Pseudomonas Putida
Keywords keywords	PqqB, PQQ, metallo-beta-lactamase, beta-lactamase, Pyrroloquinoline quinone, HORMONE; HORMONE
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.

4z67__assembly_1__model_1

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

Download this curve (.dat)

4z67__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4z67__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.73 Å
Rg (electron density)	24.83 Å
Total Rg	25.55 Å
Atom count	4804
Residues	618
Excluded volume	84595 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4z67__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 (6)

Entity 1 Entity 1 polymer

Description description	Coenzyme PQQ synthesis protein B
Molecular weight formula_weight	34123.7 kDa
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	2817

MMYIQVLGSAAGGGFPQWNCNCVNCKGYRDGTLKATARTQSSIALSDDGVHWILCNASPDIRAQLQAFAPMQPARALRDTGINAIVLLDSQIDHTTGLLSLREGCPHQVWCTDMVHQDLTTGFPLFNMLSHWNGGLQWNRIELEGSFVIDACPNLKFTPFPLRSAAPPYSPHRFDPHPGDNLGLMVEDTRTGGKLFYAPGLGQVDEKLLAMMHGADCLLVDGTLWEDDEMQRRGVGTRTGREMGHLAQNGPGGTLEVLDGFPRQRKVLIHINNTNPILDENSPERAEVLRRGVEVAFDGMSIELLEHHH

Source Source

Source organism organism	Pseudomonas putida (strain KT2440)
NCBI taxonomy ID ncbi_taxonomy_id	160488
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	318

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4z67A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

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Unit-cell length a length_a	86.327 Å
Unit-cell length b length_b	86.327 Å
Unit-cell length c length_c	107.064 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	29.350 Å
R factor r_factor	0.1444
R_work r_work	0.1428
R_free r_free	0.1743

The 1.5-angstrom crystal structure of Mn(2+)-bound PqqB from Pseudomonas Putida

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

Coenzyme PQQ synthesis protein B

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

4z67__assembly_1__model_1

4z67__assembly_1__model_1 | I(q)

4z67__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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

The 1.5-angstrom crystal structure of Mn(2+)-bound PqqB from Pseudomonas Putida

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

Coenzyme PQQ synthesis protein B

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

4z67__assembly_1__model_1

4z67__assembly_1__model_1 | I(q)

4z67__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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)