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1djq

STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)

Method: X-RAY DIFFRACTION Dmax: 100.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRIMETHYLAMINE DEHYDROGENASE

Methylophilus methylotrophus

UniProt P16099

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 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

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 1DJQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DJN STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT WILD TYPE 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）
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
1O94 Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein Deposited 2002-12-11 Different mutation/modification 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 mutation/modification 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 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）
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.

SAXS scattering curve SAXS Profile

SAXS profile for 1djq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1djq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1djq
Deposition date deposition_date1999-12-03
Structure title titleSTRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)
Keywords keywordsIRON-SULFUR FLAVOPROTEIN, ELECTRON TRANSFER, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.44 Å
Radius of gyration Rg (electron density) rg_electron31.64 Å
Forward intensity I(0) i0446394000.00
Molecular weight molecular_weight165370.0 kDa
Excluded volume excluded_volume204560 ų
Envelope volume envelope_volume238750 ų
Hydration-shell volume shell_volume58607 ų
Envelope diameter envelope_diameter105.5 Å
Shell Rg shell_rg41.45 Å
Envelope Rg envelope_rg31.78 Å
Shape Rg shape_rg31.63 Å
Total Rg total_rg32.33 Å
Total atoms total_atoms11612
Residues n_residues1458
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax100.6 Å
Rg (real space) rg_real32.18 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real4.4640e+08
I(0) uncertainty (real space) i0_real_error6.6310e+06
Rg (reciprocal space) rg_reciprocal32.30 Å
I(0) (reciprocal space) i0_reciprocal446400000.0000
Solution quality estimate total_estimate0.8174
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.1 Å
Skewness Skewness skewness0.123
Kurtosis Kurtosis kurtosis-0.442
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha218800000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1djqa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.4 — FMN-linked oxidoreductases
Family Family familyc.1.4.1 — FMN-linked oxidoreductases
Domain ID domain_idd1djqa2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.1 — C-terminal domain of adrenodoxin reductase-like
Domain ID domain_idd1djqa3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.4 — Nucleotide-binding domain
Superfamily Superfamily superfamilyc.4.1 — Nucleotide-binding domain
Family Family familyc.4.1.1 — N-terminal domain of adrenodoxin reductase-like
Domain ID domain_idd1djqb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.4 — FMN-linked oxidoreductases
Family Family familyc.1.4.1 — FMN-linked oxidoreductases
Domain ID domain_idd1djqb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.1 — C-terminal domain of adrenodoxin reductase-like
Domain ID domain_idd1djqb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.4 — Nucleotide-binding domain
Superfamily Superfamily superfamilyc.4.1 — Nucleotide-binding domain
Family Family familyc.4.1.1 — N-terminal domain of adrenodoxin reductase-like

CATH v4.4 (6 domains)

Domain ID domain_id1djqA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id1djqA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1djqA03
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1djqB01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id1djqB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1djqB03
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
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8. Citations (2)

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9. Files and Curves (10)