+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ggm | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of LpxI | ||||||
![]() | UDP-2,3-diacylglucosamine pyrophosphatase LpxI | ||||||
![]() | HYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / lipid binding | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Metzger IV, L.E. / Lee, J.K. / Finer-Moore, J.S. / Raetz, C.R.H. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP) | ||||||
![]() | ![]() Title: LpxI structures reveal how a lipid A precursor is synthesized. Authors: Metzger, L.E. / Lee, J.K. / Finer-Moore, J.S. / Raetz, C.R. / Stroud, R.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 118.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 99.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 813.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 822.4 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | Biochemical, analytical, and mass spec data suggests dimer, which is noted in the manuscript, but it can also be monomer based on crystallographic results. |
-
Components
#1: Protein | Mass: 30376.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B8GWR0, UniProt: A0A0H3C8Q1*PLUS, UDP-2,3-diacylglucosamine diphosphatase |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-LP5 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.29 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 100 mM MES pH 5.7, 3-7% w/v PEG 6000, 2.5% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2009 / Details: Double Crystals Si111 |
Radiation | Monochromator: DoubleCrystalSi111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→45 Å / Num. all: 11975 / Num. obs: 11932 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.8971→3.1886 Å / % possible all: 99.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.217 Å2 / ksol: 0.333 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.897→45.513 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 19.5091 Å / Origin y: -34.0188 Å / Origin z: 22.8347 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |