SAXSdb — 6icm

▼

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

Methylxanthine N1-demethylase NdmA

Pseudomonas putida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Oxidoreductase NdmD × 2 （H9N291） FE2/S2 (INORGANIC) CLUSTER × 8 FE (III) ION × 6 TETRAETHYLENE GLYCOL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NDMA_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–369； UniProt 1–351 Author chain B； PDBConstruct 19–369； UniProt 1–351 Author chain C； PDBConstruct 19–369； UniProt 1–351

Oxidoreductase NdmD

Pseudomonas putida

UniProt H9N291

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Methylxanthine N1-demethylase NdmA × 6 （H9N289） FE2/S2 (INORGANIC) CLUSTER × 8 FE (III) ION × 6 TETRAETHYLENE GLYCOL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NDMD_PSEPU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–87； UniProt 502–588

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6icm
Deposition date deposition_date	2018-09-06
Structure title title	Pseudomonas putida CBB5 NdmA with ferredoxin domain of NdmD
Keywords keywords	N-demethylase, Rieske oxygenase, reductase plant type ferredoxin, METAL BINDING PROTEIN-OXIDOREDUCTASE complex; METAL BINDING PROTEIN/OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6icm__assembly_1__model_1

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

Download this curve (.dat)

6icm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6icm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.74 Å
Rg (electron density)	42.82 Å
Total Rg	43.27 Å
Atom count	17500
Residues	2154
Excluded volume	309020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6icm__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Methylxanthine N1-demethylase NdmA
Molecular weight formula_weight	42379.4 kDa
EC 编号 ec_number	1.14.13.178
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8753

MGSSHHHHHHENLYFQGSMEQAIINDEREYLRHFWHPVCTVTELEKAHPSSLGPLAVKLLNEQLVVAKLGDEYVAMRDRCAHRSAKLSLGTVSGNRLQCPYHGWQYDTHGACQLVPACPNSPIPNKAKVDRFDCEERYGLIWIRLDSSFDCTEIPYFSAANDPRLRIVIQEPYWWDATAERRWENFTDFSHFAFIHPGTLFDPNNAEPPIVPMDRFNGQFRFVYDTPEDMAVPNQAPIGSFSYTCSMPFAINLEVSKYSSSSLHVLFNVSCPVDSHTTKNFLIFAREQSDDSDYLHIAFNDLVFAEDKPVIESQWPKDAPADEVSVVADKVSIQYRKWLRELKEAHKEGSQAFRSALLDPVIESDRSYI

Source Source

Source organism organism	Pseudomonas putida
Common name common_name	Arthrobacter siderocapsulatus
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Oxidoreductase NdmD
Molecular weight formula_weight	9659.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

EYEVELKKTGQIFTVSPGSTLLQACLDNDVRIEASCEQGVCGTCITPVVSGDLEHHDTYLSKKERESGKWIMPCVSRCKSKKIVLDL

Source Source

Source organism organism	Pseudomonas putida
Common name common_name	Arthrobacter siderocapsulatus
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 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	3

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6icmD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

▶

Unit-cell length a length_a	118.265 Å
Unit-cell length b length_b	118.265 Å
Unit-cell length c length_c	455.692 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.961 Å
Low-resolution limit resolution_low	42.460 Å
R factor r_factor	0.2065
R_work r_work	0.2036
R_free r_free	0.2612

Pseudomonas putida CBB5 NdmA with ferredoxin domain of NdmD

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

Methylxanthine N1-demethylase NdmA

State in the Current Structure

Other States of the Same Protein in the Database

Oxidoreductase NdmD

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

6icm__assembly_1__model_1

6icm__assembly_1__model_1 | I(q)

6icm__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 polymer

Polymer Polymer

Source Source

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)

Pseudomonas putida CBB5 NdmA with ferredoxin domain of NdmD

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

Methylxanthine N1-demethylase NdmA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Oxidoreductase NdmD

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

6icm__assembly_1__model_1

6icm__assembly_1__model_1 | I(q)

6icm__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 polymer

Polymer Polymer

Source Source

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)