3orv

Crystal Structure of the Y294H-MauG/pre-Methylamine Dehydrogenase Complex

Method: X-RAY DIFFRACTION Dmax: 162.5 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 Mutation:Y294H Methylamine dehydrogenase light chain × 2 (P22619) Methylamine dehydrogenase heavy chain × 2 (A1BB97) CA CALCIUM ION × 2 HEC HEME C × 4 EDO 1,2-ETHANEDIOL × 3 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 PG4 TETRAETHYLENE GLYCOL × 2 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;293 K;Drops contained 1uL protein with 2uL reservoir solution. Protein solution: 100uM Y294H-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 24-26 % w/v PEG 8000, 0.1 M sodium acetate, 0.1 M MES pH 6.4., VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.91 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 Mutation:Trp57 is hydroxylated at C7 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 HEC HEME C × 4 EDO 1,2-ETHANEDIOL × 3 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 PG4 TETRAETHYLENE GLYCOL × 2 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;293 K;Drops contained 1uL protein with 2uL reservoir solution. Protein solution: 100uM Y294H-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 24-26 % w/v PEG 8000, 0.1 M sodium acetate, 0.1 M MES pH 6.4., VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.91 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 HEC HEME C × 4 EDO 1,2-ETHANEDIOL × 3 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 PG4 TETRAETHYLENE GLYCOL × 2 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.4;293 K;Drops contained 1uL protein with 2uL reservoir solution. Protein solution: 100uM Y294H-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 24-26 % w/v PEG 8000, 0.1 M sodium acetate, 0.1 M MES pH 6.4., VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.91 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 3orv

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3orv
Deposition date deposition_date2010-09-07
Structure title titleCrystal Structure of the Y294H-MauG/pre-Methylamine Dehydrogenase Complex
Keywords keywordsMauG, methylamine dehydrogenase, His-His heme, c-heme, quinone cofactor, 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_guinier42.52
Radius of gyration Rg (electron density) rg_electron42.58
Forward intensity I(0) i01088890000.00
Molecular weight molecular_weight178400.0 kDa
Excluded volume excluded_volume171350 ų
Envelope volume envelope_volume300600 ų
Hydration-shell volume shell_volume61204 ų
Envelope diameter envelope_diameter173.5
Shell Rg shell_rg45.28
Envelope Rg envelope_rg42.84
Shape Rg shape_rg42.56
Total Rg total_rg42.69
Total atoms total_atoms13477
Residues n_residues1707
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 dmax162.5
Rg (real space) rg_real42.85
Rg uncertainty (real space) rg_real_error2.16
I(0) (real space) i0_real1.0890e+09
I(0) uncertainty (real space) i0_real_error2.1280e+07
Rg (reciprocal space) rg_reciprocal42.52
I(0) (reciprocal space) i0_reciprocal1088000000.0000
Solution quality estimate total_estimate0.8051
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.9
Skewness Skewness skewness0.622
Kurtosis Kurtosis kurtosis0.168
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha111000000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.582; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.788; Smooth: 0.927

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3orvc_
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_idd3orvd_
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_idd3orve_
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_idd3orvf_
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_id3orvA01
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_id3orvA02
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_id3orvB01
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_id3orvB02
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_id3orvC00
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_id3orvD00
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_id3orvE00
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_id3orvF00
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)