4o1q

Crystal Structure of the Q103N-MauG/pre-Methylamine Dehydrogenase Complex

Method: X-RAY DIFFRACTION Dmax: 165.3 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:Q103N Methylamine dehydrogenase light chain × 2 (A1BBA0) Methylamine dehydrogenase heavy chain × 2 (A1BB97) CA CALCIUM ION × 2 HEC HEME C × 4 EDO 1,2-ETHANEDIOL × 3 PO4 PHOSPHATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;0.1 M MES, pH 6.4, 0.1 M sodium acetate, 24-30% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.59 Å R-free 0.254

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 7–373; UniProt 21–387 Author chain B; PDBConstruct 7–373; UniProt 21–387

Methylamine dehydrogenase light chain

Paracoccus denitrificans

UniProt A1BBA0

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 HEC HEME C × 4 EDO 1,2-ETHANEDIOL × 3 PO4 PHOSPHATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;0.1 M MES, pH 6.4, 0.1 M sodium acetate, 24-30% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.59 Å R-free 0.254

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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A1BBA0_PARDP
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 7–137; UniProt 58–188 Author chain E; PDBConstruct 7–137; 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 33–417 Chain F; UniProt 33–417 Fragment:UNP residues 33-417 Methylamine utilization protein MauG × 2 (Q51658) Methylamine dehydrogenase light chain × 2 (A1BBA0) CA CALCIUM ION × 2 HEC HEME C × 4 EDO 1,2-ETHANEDIOL × 3 PO4 PHOSPHATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;0.1 M MES, pH 6.4, 0.1 M sodium acetate, 24-30% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.59 Å R-free 0.254

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 1–385; UniProt 33–417 Author chain F; PDBConstruct 1–385; UniProt 33–417

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 4o1q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4o1q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4o1q
Deposition date deposition_date2013-12-16
Structure title titleCrystal Structure of the Q103N-MauG/pre-Methylamine Dehydrogenase Complex
Keywords keywordsOXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.51
Radius of gyration Rg (electron density) rg_electron42.63
Forward intensity I(0) i01087740000.00
Molecular weight molecular_weight178210.0 kDa
Excluded volume excluded_volume171090 ų
Envelope volume envelope_volume292800 ų
Hydration-shell volume shell_volume59959 ų
Envelope diameter envelope_diameter173.7
Shell Rg shell_rg44.89
Envelope Rg envelope_rg42.92
Shape Rg shape_rg42.62
Total Rg total_rg42.74
Total atoms total_atoms13457
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 dmax165.3
Rg (real space) rg_real42.89
Rg uncertainty (real space) rg_real_error1.84
I(0) (real space) i0_real1.0880e+09
I(0) uncertainty (real space) i0_real_error2.0050e+07
Rg (reciprocal space) rg_reciprocal42.51
I(0) (reciprocal space) i0_reciprocal1087000000.0000
Solution quality estimate total_estimate0.7893
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.2
Skewness Skewness skewness0.646
Kurtosis Kurtosis kurtosis0.181
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha101800000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.530; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.714; Smooth: 0.953

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (11)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4o1qc_
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_idd4o1qe_
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

CATH v4.4 (8 domains)

Domain ID domain_id4o1qA01
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_id4o1qA02
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_id4o1qB01
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_id4o1qB02
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_id4o1qC00
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_id4o1qD00
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_id4o1qE00
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_id4o1qF00
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)