3sxt

Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of MauG

Method: X-RAY DIFFRACTION Dmax: 162.3 Å Quality: REASONABLE

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

Methylamine utilization protein MauG

Paracoccus denitrificans

UniProt Q51658

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 21–387 Chain B; UniProt 21–387 Fragment:UNP residues 21-387 Methylamine dehydrogenase light chain × 2 (P22619) Methylamine dehydrogenase heavy chain × 2 (A1BB97) CA CALCIUM ION × 2 NA SODIUM ION × 4 HEC HEME C × 4 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;293 K;Drops contained 1uL protein with 3uL reservoir solution. WT-MauG and MADH were each reduced in an anaerobic glove box prior to preparing the protein mixture for crystallization. Protein mixture: 100uM reduced WT-MauG and 50uM reduced MADH in 10mM potassium phosphate pH7.5 with 2mM sodium dithionite. Reservoir solution contained: 22% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.4 and 2mM sodium dithionite. Crystallization was carried out in an anaerobic glove box at ambient temperature., VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.81 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.

27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MAUG_PARDP
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–367; UniProt 21–387 Author chain B; PDBConstruct 1–367; UniProt 21–387

Methylamine dehydrogenase light chain

Paracoccus denitrificans

UniProt P22619

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 58–188 Chain E; UniProt 58–188 Fragment:UNP residues 58-188 Non-standard monomer:Yes (specific site not provided by mmCIF) Methylamine utilization protein MauG × 2 (Q51658) Methylamine dehydrogenase heavy chain × 2 (A1BB97) CA CALCIUM ION × 2 NA SODIUM ION × 4 HEC HEME C × 4 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;293 K;Drops contained 1uL protein with 3uL reservoir solution. WT-MauG and MADH were each reduced in an anaerobic glove box prior to preparing the protein mixture for crystallization. Protein mixture: 100uM reduced WT-MauG and 50uM reduced MADH in 10mM potassium phosphate pH7.5 with 2mM sodium dithionite. Reservoir solution contained: 22% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.4 and 2mM sodium dithionite. Crystallization was carried out in an anaerobic glove box at ambient temperature., VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.81 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.

28 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DHML_PARDE
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–131; UniProt 58–188 Author chain E; PDBConstruct 1–131; UniProt 58–188

Methylamine dehydrogenase heavy chain

Paracoccus denitrificans

UniProt A1BB97

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 32–417 Chain F; UniProt 32–417 Fragment:UNP residues 32-417 Methylamine utilization protein MauG × 2 (Q51658) Methylamine dehydrogenase light chain × 2 (P22619) CA CALCIUM ION × 2 NA SODIUM ION × 4 HEC HEME C × 4 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;293 K;Drops contained 1uL protein with 3uL reservoir solution. WT-MauG and MADH were each reduced in an anaerobic glove box prior to preparing the protein mixture for crystallization. Protein mixture: 100uM reduced WT-MauG and 50uM reduced MADH in 10mM potassium phosphate pH7.5 with 2mM sodium dithionite. Reservoir solution contained: 22% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.4 and 2mM sodium dithionite. Crystallization was carried out in an anaerobic glove box at ambient temperature., VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.81 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.

27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A1BB97_PARDP
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–386; UniProt 32–417 Author chain F; PDBConstruct 1–386; UniProt 32–417

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 3sxt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3sxt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3sxt
Deposition date deposition_date2011-07-15
Structure title titleCrystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of MauG
Keywords keywordsMauG, methylamine dehydrogenase, TTQ, c-heme, OXIDOREDUCTASE-ELECTRON TRANSPORT complex; OXIDOREDUCTASE/ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.75
Radius of gyration Rg (electron density) rg_electron42.74
Forward intensity I(0) i0570103000.00
Molecular weight molecular_weight190810.0 kDa
Excluded volume excluded_volume236170 ų
Envelope volume envelope_volume298390 ų
Hydration-shell volume shell_volume60549 ų
Envelope diameter envelope_diameter174.5
Shell Rg shell_rg45.34
Envelope Rg envelope_rg43.12
Shape Rg shape_rg42.73
Total Rg total_rg42.89
Total atoms total_atoms13439
Residues n_residues1710
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax162.3
Rg (real space) rg_real43.10
Rg uncertainty (real space) rg_real_error2.07
I(0) (real space) i0_real5.7010e+08
I(0) uncertainty (real space) i0_real_error1.1500e+07
Rg (reciprocal space) rg_reciprocal42.76
I(0) (reciprocal space) i0_reciprocal569900000.0000
Solution quality estimate total_estimate0.5894
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.9
Skewness Skewness skewness0.619
Kurtosis Kurtosis kurtosis0.136
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha108200000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.593; Stabil: 1.000; Sysdev: 0.083; Positv: 1.000; Valcen: 0.791; Smooth: 0.839

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3sxtc_
Class classg — Small proteins
Fold Fold foldg.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamilyg.21.1 — Methylamine dehydrogenase, L chain
Family Family familyg.21.1.1 — Methylamine dehydrogenase, L chain
Domain ID domain_idd3sxtd_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Family Family familyb.69.2.0 — automated matches
Domain ID domain_idd3sxte_
Class classg — Small proteins
Fold Fold foldg.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamilyg.21.1 — Methylamine dehydrogenase, L chain
Family Family familyg.21.1.1 — Methylamine dehydrogenase, L chain
Domain ID domain_idd3sxtf_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Family Family familyb.69.2.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id3sxtA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id3sxtA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id3sxtB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id3sxtB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id3sxtC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily10 — Methylamine/Aralkylamine dehydrogenase light chain
Domain ID domain_id3sxtD00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id3sxtE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily10 — Methylamine/Aralkylamine dehydrogenase light chain
Domain ID domain_id3sxtF00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

8. Citations (1)

9. Files and Curves (10)