3k9z

Rational Design of a Structural and Functional Nitric Oxide Reductase

Method: X-RAY DIFFRACTION Dmax: 50.4 Å Quality: GOOD

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

Myoglobin

Physeter catodon

UniProt P02185

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 Mutation:L29H, F43H, V68E HEM PROTOPORPHYRIN IX CONTAINING FE × 1 FE2 FE (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 7;298 K;pH 7, EVAPORATION, temperature 298K Resolution 1.72 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.

354 other PDB entries and 366 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYG_PHYCA
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 3k9z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3k9z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3k9z
Deposition date deposition_date2009-10-16
Structure title titleRational Design of a Structural and Functional Nitric Oxide Reductase
Keywords keywordsAlpha HELIX, Heme, Iron, Metal-binding, Oxygen transport, Nitric Oxide Reduction; OXYGEN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.33
Radius of gyration Rg (electron density) rg_electron15.08
Forward intensity I(0) i05788030.00
Molecular weight molecular_weight17900.0 kDa
Excluded volume excluded_volume22591 ų
Envelope volume envelope_volume24696 ų
Hydration-shell volume shell_volume13884 ų
Envelope diameter envelope_diameter50.2
Shell Rg shell_rg20.92
Envelope Rg envelope_rg15.32
Shape Rg shape_rg15.07
Total Rg total_rg16.19
Total atoms total_atoms1263
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 dmax50.4
Rg (real space) rg_real16.22
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real5.7880e+06
I(0) uncertainty (real space) i0_real_error6.4240e+04
Rg (reciprocal space) rg_reciprocal16.23
I(0) (reciprocal space) i0_reciprocal5788000.0000
Solution quality estimate total_estimate0.8208
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.7
Skewness Skewness skewness0.122
Kurtosis Kurtosis kurtosis-0.444
Angular range angular_range— – 0.4850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1036000.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3k9za_
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_id3k9zA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins

8. Citations (1)

9. Files and Curves (10)