4fma

EspG structure

Method: X-RAY DIFFRACTION Dmax: 223.6 Å Quality: GOOD

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

EspG protein

Escherichia coli

UniProt Q5WMC0

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 47–397 Not recorded MG MAGNESIUM ION × 2 FMT FORMIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
10 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain J; UniProt 47–397 Not recorded MG MAGNESIUM ION × 2 ACY ACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
11 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain K; UniProt 47–397 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
12 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain L; UniProt 47–397 Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
13 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 47–397 Chain C; UniProt 47–397 Not recorded MG MAGNESIUM ION × 4 FMT FORMIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
14 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 47–397 Chain F; UniProt 47–397 Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
15 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 47–397 Chain K; UniProt 47–397 Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
16 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 47–397 Chain I; UniProt 47–397 Not recorded MG MAGNESIUM ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
17 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 47–397 Chain L; UniProt 47–397 Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
18 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 47–397 Chain J; UniProt 47–397 Not recorded MG MAGNESIUM ION × 3 ACY ACETIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 47–397 Not recorded MG MAGNESIUM ION × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 47–397 Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 47–397 Not recorded MG MAGNESIUM ION × 3 FMT FORMIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 47–397 Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 47–397 Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
7 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain G; UniProt 47–397 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
8 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain H; UniProt 47–397 Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239
9 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain I; UniProt 47–397 Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;2.5 M sodium formate, 0.1 M Bis-Tis propane (pH 7.0), and 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.15 Å R-free 0.239

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.

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5WMC0_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–351; UniProt 47–397 Author chain B; PDBConstruct 1–351; UniProt 47–397 Author chain C; PDBConstruct 1–351; UniProt 47–397 Author chain D; PDBConstruct 1–351; UniProt 47–397 Author chain E; PDBConstruct 1–351; UniProt 47–397 Author chain F; PDBConstruct 1–351; UniProt 47–397 Author chain G; PDBConstruct 1–351; UniProt 47–397 Author chain H; PDBConstruct 1–351; UniProt 47–397 Author chain I; PDBConstruct 1–351; UniProt 47–397 Author chain J; PDBConstruct 1–351; UniProt 47–397 Author chain K; PDBConstruct 1–351; UniProt 47–397 Author chain L; PDBConstruct 1–351; UniProt 47–397

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 4fma

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fma
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fma
Deposition date deposition_date2012-06-16
Structure title titleEspG structure
Keywords keywordsalpha and beta fold, Rab1 GAP, Rab1 GTPase, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier64.14
Radius of gyration Rg (electron density) rg_electron63.94
Forward intensity I(0) i03205660000.00
Molecular weight molecular_weight457420.0 kDa
Excluded volume excluded_volume565050 ų
Envelope volume envelope_volume899690 ų
Hydration-shell volume shell_volume119170 ų
Envelope diameter envelope_diameter207.4
Shell Rg shell_rg63.01
Envelope Rg envelope_rg61.81
Shape Rg shape_rg63.94
Total Rg total_rg63.91
Total atoms total_atoms32039
Residues n_residues4153
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 dmax223.6
Rg (real space) rg_real63.97
Rg uncertainty (real space) rg_real_error2.17
I(0) (real space) i0_real3.2060e+09
I(0) uncertainty (real space) i0_real_error6.5890e+07
Rg (reciprocal space) rg_reciprocal64.25
I(0) (reciprocal space) i0_reciprocal3207000000.0000
Solution quality estimate total_estimate0.8851
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary74.5
Skewness Skewness skewness0.166
Kurtosis Kurtosis kurtosis-0.566
Angular range angular_range— – 0.1200 −1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha95550000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.933

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id4fmaA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaE01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaF01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaG01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaH01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaI01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaJ01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaK01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain
Domain ID domain_id4fmaL01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily460 — EspG protein, N-terminal domain

8. Citations (1)

9. Files and Curves (10)