1fyz

METHANE MONOOXYGENASE HYDROXYLASE, FORM II REDUCED BY SOAKING

Method: X-RAY DIFFRACTION Dmax: 128.5 Å Quality: GOOD

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

METHANE MONOOXYGENASE COMPONENT A, ALPHA CHAIN

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 A; UniProt 1–527 Chain B; UniProt 1–527 Not recorded METHANE MONOOXYGENASE COMPONENT A, BETA CHAIN × 2 (P18798) METHANE MONOOXYGENASE COMPONENT A, GAMMA CHAIN × 2 (P11987) FE2 FE (II) ION × 4 CA CALCIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298 K Resolution 2.15 Å R-free 0.230

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 A; PDBConstruct 1–527; UniProt 1–527 Author chain B; PDBConstruct 1–527; UniProt 1–527

METHANE MONOOXYGENASE COMPONENT A, BETA CHAIN

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 C; UniProt 1–389 Chain D; UniProt 1–389 Not recorded METHANE MONOOXYGENASE COMPONENT A, ALPHA CHAIN × 2 (P22869) METHANE MONOOXYGENASE COMPONENT A, GAMMA CHAIN × 2 (P11987) FE2 FE (II) ION × 4 CA CALCIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298 K Resolution 2.15 Å R-free 0.230

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 C; PDBConstruct 1–389; UniProt 1–389 Author chain D; PDBConstruct 1–389; UniProt 1–389

METHANE MONOOXYGENASE COMPONENT A, GAMMA CHAIN

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 E; UniProt 1–170 Chain F; UniProt 1–170 Not recorded METHANE MONOOXYGENASE COMPONENT A, ALPHA CHAIN × 2 (P22869) METHANE MONOOXYGENASE COMPONENT A, BETA CHAIN × 2 (P18798) FE2 FE (II) ION × 4 CA CALCIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298 K Resolution 2.15 Å R-free 0.230

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 E; PDBConstruct 1–170; UniProt 1–170 Author chain F; PDBConstruct 1–170; UniProt 1–170

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 1fyz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1fyz
Deposition date deposition_date2000-10-03
Structure title titleMETHANE MONOOXYGENASE HYDROXYLASE, FORM II REDUCED BY SOAKING
Keywords keywordsdinuclear iron center, monooxygenase, oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.42
Radius of gyration Rg (electron density) rg_electron41.04
Forward intensity I(0) i0892727000.00
Molecular weight molecular_weight247620.0 kDa
Excluded volume excluded_volume309300 ų
Envelope volume envelope_volume364030 ų
Hydration-shell volume shell_volume70476 ų
Envelope diameter envelope_diameter135.6
Shell Rg shell_rg48.82
Envelope Rg envelope_rg40.98
Shape Rg shape_rg41.02
Total Rg total_rg41.45
Total atoms total_atoms17514
Residues n_residues2132
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 dmax128.5
Rg (real space) rg_real41.38
Rg uncertainty (real space) rg_real_error0.96
I(0) (real space) i0_real8.9270e+08
I(0) uncertainty (real space) i0_real_error1.5740e+07
Rg (reciprocal space) rg_reciprocal41.42
I(0) (reciprocal space) i0_reciprocal892800000.0000
Solution quality estimate total_estimate0.8709
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.0
Skewness Skewness skewness0.275
Kurtosis Kurtosis kurtosis-0.589
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha434600000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.463

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1fyza_
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_idd1fyzb_
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_idd1fyzc_
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_idd1fyzd_
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_idd1fyze_
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_idd1fyzf_
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_id1fyzA00
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_id1fyzB00
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_id1fyzC00
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_id1fyzD00
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_id1fyzE01
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_id1fyzE02
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_id1fyzF01
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_id1fyzF02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily30 — Methane monooxygenase, gamma chain, domain 2

8. Citations (1)

9. Files and Curves (10)