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3bs6

1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC

Method: X-RAY DIFFRACTION Dmax: 79.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Inner membrane protein oxaA

Escherichia coli

UniProt P25714

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 56–329 Fragment：UNP residues 56-329 Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 5 PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；293 K；21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K Resolution 1.80 Å R-free 0.213
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 56–329 Fragment：UNP residues 56-329 Non-standard monomer：Yes (specific site not provided by mmCIF) PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 4 2PE NONAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；293 K；21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K Resolution 1.80 Å R-free 0.213
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 56–329 Chain B； UniProt 56–329 Fragment：UNP residues 56-329 Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 10 PG4 TETRAETHYLENE GLYCOL × 2 PGE TRIETHYLENE GLYCOL × 6 EDO 1,2-ETHANEDIOL × 14 2PE NONAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；293 K；21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K Resolution 1.80 Å R-free 0.213

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.

Other PDB Difference from Current Entry 3BS6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BLC Crystal structure of the periplasmic domain of the Escherichia Coli YIDC Deposited 2007-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–340（315 aa） Fragment：UNP residues 26-340
Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.1；295 K；0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.50 Å R-free 0.249
3BLC Crystal structure of the periplasmic domain of the Escherichia Coli YIDC Deposited 2007-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–340（315 aa） Fragment：UNP residues 26-340
Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.1；295 K；0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.50 Å R-free 0.249
3BLC Crystal structure of the periplasmic domain of the Escherichia Coli YIDC Deposited 2007-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 26–340（315 aa） Fragment：UNP residues 26-340
Chain B 26–340（315 aa） Fragment：UNP residues 26-340
Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.1；295 K；0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.50 Å R-free 0.249
4UTQ A structural model of the active ribosome-bound membrane protein insertase YidC Deposited 2014-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–548（548 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV,
Resolution 8.00 Å
5MG3 EM fitted model of bacterial holo-translocon Deposited 2016-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 2–548（547 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
9RBF Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the membrane protein insertase SecYEG-YidC Deposited 2025-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 61-meric
Chain 9 1–548（548 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.44 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OXAA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–274； UniProt 56–329 Author chain B； PDBConstruct 1–274； UniProt 56–329

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 3bs6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bs6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bs6
Deposition date deposition_date2007-12-22
Structure title title1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC
Keywords keywords;YIDC/OXA1/ALB3 family, Membrane insertion, Chaperone, SEC translocon, Periplasmic domain, Beta supersandwich fold, Helical linker domain, MEMBRANE PROTEIN, PROTEIN TRANSPORT ;; MEMBRANE PROTEIN, PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.50 Å
Radius of gyration Rg (electron density) rg_electron24.41 Å
Forward intensity I(0) i056656300.00
Molecular weight molecular_weight58310.0 kDa
Excluded volume excluded_volume72704 ų
Envelope volume envelope_volume87682 ų
Hydration-shell volume shell_volume29510 ų
Envelope diameter envelope_diameter81.5 Å
Shell Rg shell_rg32.08 Å
Envelope Rg envelope_rg24.50 Å
Shape Rg shape_rg24.40 Å
Total Rg total_rg25.27 Å
Total atoms total_atoms4078
Residues n_residues510
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax79.9 Å
Rg (real space) rg_real25.42 Å
Rg uncertainty (real space) rg_real_error0.41 Å
I(0) (real space) i0_real5.6660e+07
I(0) uncertainty (real space) i0_real_error7.2680e+05
Rg (reciprocal space) rg_reciprocal25.45 Å
I(0) (reciprocal space) i0_reciprocal56660000.0000
Solution quality estimate total_estimate0.9067
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary78.6 Å
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.465
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9846000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.975
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3bs6A00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily90 —
Domain ID domain_id3bs6B00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily90 —
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8. Citations (1)

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9. Files and Curves (10)