3iqm

Active site mutants of B. subtilis SecA

Method: X-RAY DIFFRACTION Dmax: 109.0 Å Quality: GOOD

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

Protein translocase subunit secA

Bacillus subtilis subsp. subtilis

UniProt P28366

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–802 Fragment:UNP residues 1-802 Mutation:E208Q SO4 SULFATE ION × 22 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;299 K;20 mM BES pH 7.0, 2.12 M Ammonium sulfate, 31% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 299K Resolution 3.40 Å R-free 0.267

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.

16 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SECA_BACSU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–802; UniProt 1–802

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 3iqm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3iqm
Deposition date deposition_date2009-08-20
Structure title titleActive site mutants of B. subtilis SecA
Keywords keywords;alpha-beta protein, ATP-binding, Cell membrane, Membrane, Metal-binding, Nucleotide-binding, Protein transport, Translocation, Transport ;; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.29
Radius of gyration Rg (electron density) rg_electron33.17
Forward intensity I(0) i0143595000.00
Molecular weight molecular_weight92283.0 kDa
Excluded volume excluded_volume114200 ų
Envelope volume envelope_volume151990 ų
Hydration-shell volume shell_volume38961 ų
Envelope diameter envelope_diameter110.8
Shell Rg shell_rg39.14
Envelope Rg envelope_rg33.13
Shape Rg shape_rg33.17
Total Rg total_rg33.65
Total atoms total_atoms6456
Residues n_residues802
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 dmax109.0
Rg (real space) rg_real33.40
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real1.4360e+08
I(0) uncertainty (real space) i0_real_error2.5320e+06
Rg (reciprocal space) rg_reciprocal33.36
I(0) (reciprocal space) i0_reciprocal143600000.0000
Solution quality estimate total_estimate0.8836
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.1
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.522
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33080000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.865

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id3iqmA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3iqmA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1440 — Pre-protein croslinking domain of SecA
Homologous superfamily homologous superfamily10 — SecA, preprotein cross-linking domain
Domain ID domain_id3iqmA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3iqmA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology3060 — Helical scaffold and wing domains of SecA
Homologous superfamily homologous superfamily10 — Helical scaffold and wing domains of SecA
Domain ID domain_id3iqmA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily230

8. Citations (1)

9. Files and Curves (10)