2fae

Crystal structure of E. coli decanoyl-ACP

Method: X-RAY DIFFRACTION Dmax: 60.2 Å Quality: GOOD

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

Acyl carrier protein

Escherichia coli

UniProt P0A6A8

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 1–77 Not recorded ZN ZINC ION × 7 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
10 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–77 Chain B; UniProt 1–77 Not recorded ZN ZINC ION × 8 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
11 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–77 Not recorded ZN ZINC ION × 14 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–77 Not recorded ZN ZINC ION × 1 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–77 Chain B; UniProt 1–77 Not recorded ZN ZINC ION × 16 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
4 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–77 Chain B; UniProt 1–77 Not recorded ZN ZINC ION × 16 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
5 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–77 Chain B; UniProt 1–77 Not recorded ZN ZINC ION × 16 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
6 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–77 Chain B; UniProt 1–77 Not recorded ZN ZINC ION × 16 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
7 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–77 Chain B; UniProt 1–77 Not recorded ZN ZINC ION × 16 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
8 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–77 Chain B; UniProt 1–77 Not recorded ZN ZINC ION × 8 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269
9 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–77 Chain B; UniProt 1–77 Not recorded ZN ZINC ION × 8 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;290 K;8-12% PEG 4000, 30 mM zinc acetate, 50 mM sodium cocadylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K Resolution 1.55 Å R-free 0.269

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.

39 other PDB entries and 59 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACP_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–77; UniProt 1–77 Author chain B; PDBConstruct 1–77; UniProt 1–77

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 2fae

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2fae
Deposition date deposition_date2005-12-07
Structure title titleCrystal structure of E. coli decanoyl-ACP
Keywords keywordsacyl carrier protein, acyl chain binding, fatty acid biosynthesis, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.45
Radius of gyration Rg (electron density) rg_electron17.46
Forward intensity I(0) i07016760.00
Molecular weight molecular_weight18085.0 kDa
Excluded volume excluded_volume21957 ų
Envelope volume envelope_volume26757 ų
Hydration-shell volume shell_volume13561 ų
Envelope diameter envelope_diameter60.0
Shell Rg shell_rg22.42
Envelope Rg envelope_rg17.50
Shape Rg shape_rg17.43
Total Rg total_rg18.33
Total atoms total_atoms1238
Residues n_residues154
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 dmax60.2
Rg (real space) rg_real18.45
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real7.0170e+06
I(0) uncertainty (real space) i0_real_error9.4770e+04
Rg (reciprocal space) rg_reciprocal18.45
I(0) (reciprocal space) i0_reciprocal7017000.0000
Solution quality estimate total_estimate0.8024
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.6
Skewness Skewness skewness0.333
Kurtosis Kurtosis kurtosis-0.368
Angular range angular_range— – 0.4300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1395000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.812; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2faea_
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.1 — ACP-like
Family Family familya.28.1.1 — Acyl-carrier protein (ACP)
Domain ID domain_idd2faeb_
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.1 — ACP-like
Family Family familya.28.1.1 — Acyl-carrier protein (ACP)

CATH v4.4 (2 domains)

Domain ID domain_id2faeA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily10 — ACP-like
Domain ID domain_id2faeB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily10 — ACP-like

8. Citations (1)

9. Files and Curves (10)