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3blc

Crystal structure of the periplasmic domain of the Escherichia Coli YIDC

Method: X-RAY DIFFRACTION Dmax: 112.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Inner membrane protein oxaA

Escherichia coli K12

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 26–340 Fragment：UNP residues 26-340 Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 26–340 Fragment：UNP residues 26-340 Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 26–340 Chain B； UniProt 26–340 Fragment：UNP residues 26-340 Mutation：E228A, K229A, E231A, K232A, K234A Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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

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 3BLC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BS6 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC Deposited 2007-12-22 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 56–329（274 aa） 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
3BS6 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC Deposited 2007-12-22 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 56–329（274 aa） 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
3BS6 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC Deposited 2007-12-22 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 56–329（274 aa） Fragment：UNP residues 56-329
Chain B 56–329（274 aa） Fragment：UNP residues 56-329
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
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 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 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 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 2–316； UniProt 26–340 Author chain B； PDBConstruct 2–316； UniProt 26–340

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 3blc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3blc
Deposition date deposition_date2007-12-10
Structure title titleCrystal structure of the periplasmic domain of the Escherichia Coli YIDC
Keywords keywordsYidC, membrane assembly facilitator, chaperone, periplasmic domain, Inner membrane, Transmembrane, OXAA, PROTEIN TRANSPORT; CHAPERONE,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_guinier30.50 Å
Radius of gyration Rg (electron density) rg_electron29.76 Å
Forward intensity I(0) i060429400.00
Molecular weight molecular_weight61019.0 kDa
Excluded volume excluded_volume76137 ų
Envelope volume envelope_volume96977 ų
Hydration-shell volume shell_volume29163 ų
Envelope diameter envelope_diameter120.7 Å
Shell Rg shell_rg34.32 Å
Envelope Rg envelope_rg29.77 Å
Shape Rg shape_rg29.72 Å
Total Rg total_rg30.34 Å
Total atoms total_atoms4291
Residues n_residues550
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 dmax112.8 Å
Rg (real space) rg_real30.81 Å
Rg uncertainty (real space) rg_real_error1.13 Å
I(0) (real space) i0_real6.0430e+07
I(0) uncertainty (real space) i0_real_error1.1290e+06
Rg (reciprocal space) rg_reciprocal30.68 Å
I(0) (reciprocal space) i0_reciprocal60420000.0000
Solution quality estimate total_estimate0.7736
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.2 Å
Skewness Skewness skewness0.569
Kurtosis Kurtosis kurtosis-0.270
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha15400000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.525; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.487; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3blcA00
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily90 —
Domain ID domain_id3blcB00
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)