1mty

METHANE MONOOXYGENASE HYDROXYLASE FROM METHYLOCOCCUS CAPSULATUS (BATH)

Method: X-RAY DIFFRACTION Dmax: 126.0 Å Quality: GOOD

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

METHANE MONOOXYGENASE HYDROXYLASE

OrganismNot specified

UniProt P22869

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 15–526 Chain E; UniProt 15–526 Not recorded METHANE MONOOXYGENASE HYDROXYLASE × 2 (P18798) METHANE MONOOXYGENASE HYDROXYLASE × 2 (P11987) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;25 MM LI2SO4, 50 MM NH4OAC, 5% PEG 4000, IN 25 MM MOPS PH 7.0 WITH A RESERVOIR OF 20% PEG 4000 Resolution 1.70 Å

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.

31 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MEMA_METCA
Isoform
PDB entities 1
Chains and sequence ranges Author chain D; PDBConstruct 1–512; UniProt 15–526 Author chain E; PDBConstruct 1–512; UniProt 15–526

METHANE MONOOXYGENASE HYDROXYLASE

OrganismNot specified

UniProt P18798

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 B; UniProt 5–361 Chain C; UniProt 5–361 Not recorded METHANE MONOOXYGENASE HYDROXYLASE × 2 (P22869) METHANE MONOOXYGENASE HYDROXYLASE × 2 (P11987) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;25 MM LI2SO4, 50 MM NH4OAC, 5% PEG 4000, IN 25 MM MOPS PH 7.0 WITH A RESERVOIR OF 20% PEG 4000 Resolution 1.70 Å

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 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MEMB_METCA
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–357; UniProt 5–361 Author chain C; PDBConstruct 1–357; UniProt 5–361

METHANE MONOOXYGENASE HYDROXYLASE

OrganismNot specified

UniProt P11987

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 G; UniProt 3–164 Chain H; UniProt 3–164 Not recorded METHANE MONOOXYGENASE HYDROXYLASE × 2 (P22869) METHANE MONOOXYGENASE HYDROXYLASE × 2 (P18798) FE FE (III) ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7;25 MM LI2SO4, 50 MM NH4OAC, 5% PEG 4000, IN 25 MM MOPS PH 7.0 WITH A RESERVOIR OF 20% PEG 4000 Resolution 1.70 Å

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 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MEMG_METCA
Isoform
PDB entities 3
Chains and sequence ranges Author chain G; PDBConstruct 1–162; UniProt 3–164 Author chain H; PDBConstruct 1–162; UniProt 3–164

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 1mty

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1mty
Deposition date deposition_date1996-07-10
Structure title titleMETHANE MONOOXYGENASE HYDROXYLASE FROM METHYLOCOCCUS CAPSULATUS (BATH)
Keywords keywordsMETHANE MONOOXYGENASE, HYDROXYLASE, DINUCLEAR IRON CENTER MONOOXYGENASE, MONOOXYGENASE; MONOOXYGENASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.28
Radius of gyration Rg (electron density) rg_electron40.89
Forward intensity I(0) i0876992000.00
Molecular weight molecular_weight245660.0 kDa
Excluded volume excluded_volume306910 ų
Envelope volume envelope_volume357910 ų
Hydration-shell volume shell_volume69403 ų
Envelope diameter envelope_diameter133.9
Shell Rg shell_rg48.82
Envelope Rg envelope_rg40.91
Shape Rg shape_rg40.87
Total Rg total_rg41.27
Total atoms total_atoms20601
Residues n_residues2116
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 dmax126.0
Rg (real space) rg_real41.24
Rg uncertainty (real space) rg_real_error0.97
I(0) (real space) i0_real8.7700e+08
I(0) uncertainty (real space) i0_real_error1.4840e+07
Rg (reciprocal space) rg_reciprocal41.28
I(0) (reciprocal space) i0_reciprocal877000000.0000
Solution quality estimate total_estimate0.8635
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.1
Skewness Skewness skewness0.271
Kurtosis Kurtosis kurtosis-0.594
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha393600000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.329

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1mtyb_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.2 — Ribonucleotide reductase-like
Domain ID domain_idd1mtyc_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.2 — Ribonucleotide reductase-like
Domain ID domain_idd1mtyd_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.2 — Ribonucleotide reductase-like
Domain ID domain_idd1mtye_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.2 — Ribonucleotide reductase-like
Domain ID domain_idd1mtyg_
Class classa — All alpha proteins
Fold Fold folda.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamilya.23.3 — Methane monooxygenase hydrolase, gamma subunit
Family Family familya.23.3.1 — Methane monooxygenase hydrolase, gamma subunit
Domain ID domain_idd1mtyh_
Class classa — All alpha proteins
Fold Fold folda.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamilya.23.3 — Methane monooxygenase hydrolase, gamma subunit
Family Family familya.23.3.1 — Methane monooxygenase hydrolase, gamma subunit

CATH v4.4 (8 domains)

Domain ID domain_id1mtyB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
Domain ID domain_id1mtyC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
Domain ID domain_id1mtyD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
Domain ID domain_id1mtyE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily20 — Ribonucleotide Reductase, subunit A
Domain ID domain_id1mtyG01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily10 — Methane monooxygenase, gamma chain, domain 1
Domain ID domain_id1mtyG02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily30 — Methane monooxygenase, gamma chain, domain 2
Domain ID domain_id1mtyH01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily10 — Methane monooxygenase, gamma chain, domain 1
Domain ID domain_id1mtyH02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily30 — Methane monooxygenase, gamma chain, domain 2

8. Citations (2)

9. Files and Curves (10)