3pxs

Crystal Structure of Diferrous MauG in Complex with Pre-Methylamine Dehydrogenase:

Method: X-RAY DIFFRACTION Dmax: 163.2 Å Quality: GOOD

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) NA SODIUM ION × 4 HEC HEME C × 4 CA CALCIUM ION × 2 ACT ACETATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 1 PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;293 K;0.1M MES pH 6.4, 0.1M sodium acetate, 23-25 % w/v PEG 8000, vapor diffusion, hanging drop, temperature 293K , VAPOR DIFFUSION, HANGING DROP Resolution 2.22 Å R-free 0.229

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) NA SODIUM ION × 4 HEC HEME C × 4 CA CALCIUM ION × 2 ACT ACETATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 1 PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;293 K;0.1M MES pH 6.4, 0.1M sodium acetate, 23-25 % w/v PEG 8000, vapor diffusion, hanging drop, temperature 293K , VAPOR DIFFUSION, HANGING DROP Resolution 2.22 Å R-free 0.229

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) NA SODIUM ION × 4 HEC HEME C × 4 CA CALCIUM ION × 2 ACT ACETATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 1 PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;293 K;0.1M MES pH 6.4, 0.1M sodium acetate, 23-25 % w/v PEG 8000, vapor diffusion, hanging drop, temperature 293K , VAPOR DIFFUSION, HANGING DROP Resolution 2.22 Å R-free 0.229

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 3pxs

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3pxs
Deposition date deposition_date2010-12-10
Structure title titleCrystal Structure of Diferrous MauG in Complex with Pre-Methylamine Dehydrogenase:
Keywords keywordsOxidoreductase, electron transport, periplasmic space, 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_guinier42.50
Radius of gyration Rg (electron density) rg_electron42.58
Forward intensity I(0) i01081780000.00
Molecular weight molecular_weight178090.0 kDa
Excluded volume excluded_volume171190 ų
Envelope volume envelope_volume298800 ų
Hydration-shell volume shell_volume60800 ų
Envelope diameter envelope_diameter173.2
Shell Rg shell_rg45.24
Envelope Rg envelope_rg42.90
Shape Rg shape_rg42.57
Total Rg total_rg42.71
Total atoms total_atoms13452
Residues n_residues1709
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 dmax163.2
Rg (real space) rg_real42.84
Rg uncertainty (real space) rg_real_error1.98
I(0) (real space) i0_real1.0820e+09
I(0) uncertainty (real space) i0_real_error2.2180e+07
Rg (reciprocal space) rg_reciprocal42.50
I(0) (reciprocal space) i0_reciprocal1081000000.0000
Solution quality estimate total_estimate0.8030
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary158.8
Skewness Skewness skewness0.622
Kurtosis Kurtosis kurtosis0.163
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha106800000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.573; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.772; Smooth: 0.946

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3pxsc_
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_idd3pxsd_
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_idd3pxse_
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_idd3pxsf_
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_id3pxsA01
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_id3pxsA02
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_id3pxsB01
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_id3pxsB02
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_id3pxsC00
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_id3pxsD00
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_id3pxsE00
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_id3pxsF00
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)