SAXSdb — 1djn

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

TRIMETHYLAMINE DEHYDROGENASE

Methylophilus methylotrophus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–729 Chain B； UniProt 1–729	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 FMN FLAVIN MONONUCLEOTIDE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP AND MICROSEEDING；pH 6.5；295 K；PEG 8000, PHOSPHATE BUFFER, SODIUM CHLORIDE, pH 6.5, VAPOR DIFFUSION, HANGING DROP AND MICROSEEDING, temperature 295K	Resolution 2.20 Å R-free 0.185

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1DJN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DJQ STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1) Deposited 1999-12-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–729（729 aa） Chain B 1–729（729 aa）	Mutation：C30A Mutation：C30A	SF4 IRON/SULFUR CLUSTER × 2 FMN FLAVIN MONONUCLEOTIDE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion,hanging drop and microseeding；pH 6.5；295 K；PEG 8000, phosphate buffer, sodium chloride, pH 6.5, vapor diffusion,hanging drop and microseeding, temperature 295.0K	Resolution 2.20 Å R-free 0.187
1O94 Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein Deposited 2002-12-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–729（729 aa） Chain B 1–729（729 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SF4 IRON/SULFUR CLUSTER × 2 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；8% PEG 20000, 8% PEG 750 MME, 0.1-0.3 M SODIUM ACETATE, pH 6.50	Resolution 2.00 Å R-free 0.212
1O95 Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein Deposited 2002-12-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–729（729 aa） Chain B 1–729（729 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SF4 IRON/SULFUR CLUSTER × 2 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；8% PEG 20000, 8 % PEG 750 MME, 0.1-0.3 M SODIUM ACETATE, pH 6.50	Resolution 3.70 Å R-free 0.353
2TMD CORRELATION OF X-RAY DEDUCED AND EXPERIMENTAL AMINO ACID SEQUENCES OF TRIMETHYLAMINE DEHYDROGENASE Deposited 1993-10-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–729（729 aa） Chain B 1–729（729 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 2 FMN FLAVIN MONONUCLEOTIDE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHTM_METME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–729； UniProt 1–729 Author chain B； PDBConstruct 1–729； UniProt 1–729

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	1djn
Deposition date deposition_date	1999-12-03
Structure title title	STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT WILD TYPE TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)
Keywords keywords	IRON-SULFUR FLAVOPROTEIN, ELECTRON TRANSFER, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.45 Å
Radius of gyration Rg (electron density) rg_electron	31.64 Å
Forward intensity I(0) i0	446853000.00
Molecular weight molecular_weight	165370.0 kDa
Excluded volume excluded_volume	204550 Å³
Envelope volume envelope_volume	238990 Å³
Hydration-shell volume shell_volume	58634 Å³
Envelope diameter envelope_diameter	107.3 Å
Shell Rg shell_rg	41.43 Å
Envelope Rg envelope_rg	31.81 Å
Shape Rg shape_rg	31.64 Å
Total Rg total_rg	32.34 Å
Total atoms total_atoms	11612
Residues n_residues	1458
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	100.0 Å
Rg (real space) rg_real	32.19 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	4.4690e+08
I(0) uncertainty (real space) i0_real_error	6.2790e+06
Rg (reciprocal space) rg_reciprocal	32.30 Å
I(0) (reciprocal space) i0_reciprocal	446900000.0000
Solution quality estimate total_estimate	0.8956
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.9 Å
Skewness Skewness skewness	0.124
Kurtosis Kurtosis kurtosis	-0.443
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	219200000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	TRIMETHYLAMINE DEHYDROGENASE
Molecular weight formula_weight	81606.0 kDa
EC 编号 ec_number	1.5.99.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	12269

ARDPKHDILFEPIQIGPKTLRNRFYQVPHCIGAGSDKPGFQSAHRSVKAEGGWAALNTEYCSINPESDDTHRLSARIWDEGDVRNLKAMTDEVHKYGALAGVELWYGGAHAPNMESRATPRGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPLQFLNPYYNKRTDKYGGSLENRARFWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQKFVEMADSLVDMWDITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQVSKKPVLGVGRYTDPEKMIEIVTKGYADIIGCARPSIADPFLPQKVEQGRYDDIRVCIGCNVCISRWEIGGPPMICTQNATAGEEYRRGWHPEKFRQTKNKDSVLIVGAGPSGSEAARVLMESGYTVHLTDTAEKIGGHLNQVAALPGLGEWSYHRDYRETQITKLLKKNKESQLALGQKPMTADDVLQYGADKVIIATGARWNTDGTNCLTHDPIPGADASLPDQLTPEQVMDGKKKIGKRVVILNADTYFMAPSLAEKLATAGHEVTIVSGVHLANYMHFTLEYPNMMRRLHELHVEELGDHFCSRIEPGRMEIYNIWGDGSKRTYRGPGVSPRDANTSHRWIEFDSLVLVTGRHSECTLWNELKARESEWAENDIKGIYLIGDAEAPRLIADATFTGHRVAREIEEANPQIAIPYKRETIAWGTPHMPGGNFKIEYKV

来源 Source

来源生物 organism	Methylophilus methylotrophus
NCBI Class编号 ncbi_taxonomy_id	2327
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	653

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1djna1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d1djna2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.1 — C-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d1djna3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.1 — N-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d1djnb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d1djnb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.1 — C-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d1djnb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.1 — N-terminal domain of adrenodoxin reductase-like

CATH v4.4 (6 domains)

Domain ID domain_id	1djnA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1djnA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1djnA03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1djnB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1djnB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1djnB03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

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8. Citations (2)

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Unit-cell length a length_a	148.160 Å
Unit-cell length b length_b	72.000 Å
Unit-cell length c length_c	83.810 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1390
R_work r_work	0.1390
R_free r_free	0.1850

fit	/app/data/saxs_computation/dj/1djn/1djn.fit
pddf	/app/data/pr_computation/dj/1djn/1djn.pr.out
profile	/app/data/saxs_computation/dj/1djn/1djn.dat

STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT WILD TYPE TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)

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

TRIMETHYLAMINE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction