2vlx

Crystal structure of peroxymyoglobin generated by cryoradiolytic reduction of myoglobin compound III

Method: X-RAY DIFFRACTION Dmax: 52.4 Å Quality: GOOD

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

MYOGLOBIN

OrganismNot specified

UniProt P68082

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 2–154 Fragment:RESIDUES 2-154 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 PER PEROXIDE ION × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 2 PEO HYDROGEN PEROXIDE × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.8;BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 0.1 M MOPS, 5-10% OF GLYCEROL PH 6.8) Resolution 1.30 Å R-free 0.175

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.

149 other PDB entries and 156 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYG_HORSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–153; UniProt 2–154

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 2vlx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2vlx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2vlx
Deposition date deposition_date2008-01-20
Structure title titleCrystal structure of peroxymyoglobin generated by cryoradiolytic reduction of myoglobin compound III
Keywords keywords;HAEM, IRON, HEME, FERRYL, TRANSPORT, PEROXIDASE, OXYGEN TRANSPORT, OXYGEN ACTIVATION, RADIOLYTIC- REDUCTION, REACTION INTERMEDIATE, MONOOXYGENASE, METAL-BINDING, MUSCLE PROTEIN, X-RAY-INDUCED-PHOTOREDUCTION ;; OXYGEN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.77
Radius of gyration Rg (electron density) rg_electron15.25
Forward intensity I(0) i06094830.00
Molecular weight molecular_weight18078.0 kDa
Excluded volume excluded_volume22707 ų
Envelope volume envelope_volume25158 ų
Hydration-shell volume shell_volume13996 ų
Envelope diameter envelope_diameter53.4
Shell Rg shell_rg21.09
Envelope Rg envelope_rg15.53
Shape Rg shape_rg15.21
Total Rg total_rg16.47
Total atoms total_atoms1272
Residues n_residues153
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 dmax52.4
Rg (real space) rg_real16.67
Rg uncertainty (real space) rg_real_error0.32
I(0) (real space) i0_real6.0950e+06
I(0) uncertainty (real space) i0_real_error7.0560e+04
Rg (reciprocal space) rg_reciprocal16.69
I(0) (reciprocal space) i0_reciprocal6095000.0000
Solution quality estimate total_estimate0.8181
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.1
Skewness Skewness skewness0.120
Kurtosis Kurtosis kurtosis-0.450
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha939600.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2vlxa_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins

CATH v4.4 (1 domains)

Domain ID domain_id2vlxA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins

8. Citations (2)

9. Files and Curves (10)