SAXSdb — 6k3d

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

Multicopper oxidase

Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 2 CU-O-CU LINKAGE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8ZWA8_PYRAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–448； UniProt 30–477

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	6k3d
Deposition date deposition_date	2019-05-17
Structure title title	Structure of multicopper oxidase mutant
Keywords keywords	cupredoxin-like domains, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

6k3d__assembly_1__model_1

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

Download this curve (.dat)

6k3d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6k3d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.21 Å
Rg (electron density)	20.19 Å
Total Rg	21.13 Å
Atom count	3387
Residues	433
Excluded volume	60640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6k3d__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 (4)

Entity 1 Entity 1 polymer

Description description	Multicopper oxidase
Molecular weight formula_weight	49685.9 kDa
Mutation mutation	F290I
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	3631

TGEVKRPETSAPVPPLIKEATYIEATASGYMAEGVLNPTIILRRGQRVDMTLKNKLTEPTIVHWHGFDVNWHNDAHPSFAITPGESYNYSFDVVNRAGTYLYHPHPHGLTAKQFYMGQLGLVIVEDSGSDLGFKYGVNDLPLVISDRRFIGGAPVYNPTPMEMIAGFLGNAVLVNGVKDAVFKLSGGSYRLRLVNGSNARLYMLSIVKKNGDVVPMRLIAVDQGFLARPIEVRALFLAPAERAEVVVELGEGVYLLKNTPIDPMHLEMGHGMQEALPEGSEYTIATFLVEGKGEAVPVEALSDPPPEPPKPTRTRRFALSLSGMQWTINGMFWNASNPLFEHVSVEGVELWEIVNDKASMPHPMHLHGFPMWIIERKDSPRQVAELAVDNRGRLPTDLGLKDTVLIWPGETVKIVVNFDAKKRGQLFPFHCHNLEHEDGGMMINIAVK

Source Source

Source organism organism	Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
NCBI taxonomy ID ncbi_taxonomy_id	178306
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CU-O-CU LINKAGE
Molecular weight formula_weight	143.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6k3dA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	6k3dA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	6k3dA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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Unit-cell length a length_a	102.948 Å
Unit-cell length b length_b	102.948 Å
Unit-cell length c length_c	118.700 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	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	1.919 Å
Low-resolution limit resolution_low	36.933 Å
R factor r_factor	0.1770
R_work r_work	0.1753
R_free r_free	0.2099

Structure of multicopper oxidase mutant

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

Multicopper oxidase

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

6k3d__assembly_1__model_1

6k3d__assembly_1__model_1 | I(q)

6k3d__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Structure of multicopper oxidase mutant

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

Multicopper oxidase

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

6k3d__assembly_1__model_1

6k3d__assembly_1__model_1 | I(q)

6k3d__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)