UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding Similarity search - Function
Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300
BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ALTHOUGH IN THE CRYSTAL THIS MOLECULE APPEARS TO FORM A DIMER, THE MONOMER IS BIOLOGICALLY ACTIVE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
Remark 999
SEQUENCE THE RESIDUE NUMBERING SCHEME FOR THIS STRUCTURE FOLLOWS THAT OF THE E. COLI ENZYME. THIS ...SEQUENCE THE RESIDUE NUMBERING SCHEME FOR THIS STRUCTURE FOLLOWS THAT OF THE E. COLI ENZYME. THIS TREATMENT RESULTS IN A BREAK IN THE SEQUENTIAL NUMBERING IN A COUPLE OF PLACES.
Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal grow
Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM HEPES (pH 8.0), 180 mM NaCl, 10% PEG 3350, and 5 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2003 Details: a KOHZU double crystal monochromator with a sagittally focused second crystal. Two spherical mirrors, one will be rhodium coated.
Radiation
Monochromator: a KOHZU double crystal monochromator with a sagittally focused second crystal. Two spherical mirrors, one will be rhodium coated. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 2→30 Å / Num. all: 47793 / Num. obs: 47936 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.4
Reflection shell
Resolution: 2→2.07 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.9 / % possible all: 99.7
-
Processing
Software
Name
Classification
HKL-2000
datacollection
HKL-2000
datareduction
CNS
refinement
HKL-2000
datascaling
CNS
phasing
Refinement
Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→30 Å / Stereochemistry target values: Engh & Huber
Rfactor
Num. reflection
Selection details
Rfree
0.2353
2393
random
Rwork
0.1946
-
-
all
-
47936
-
obs
-
47793
-
Refine analyze
Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å
Refinement step
Cycle: LAST / Resolution: 2→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4298
0
101
410
4809
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.006
X-RAY DIFFRACTION
c_angle_deg
1.2
X-RAY DIFFRACTION
c_dihedral_angle_d
23.5
X-RAY DIFFRACTION
c_improper_angle_d
0.7
LS refinement shell
Resolution (Å)
Refine-ID
Num. reflection obs
% reflection obs (%)
2-2.07
X-RAY DIFFRACTION
4776
99.7
2.07-2.15
X-RAY DIFFRACTION
4732
99.9
2.15-2.25
X-RAY DIFFRACTION
4804
99.9
2.25-2.37
X-RAY DIFFRACTION
4758
99.9
2.37-2.52
X-RAY DIFFRACTION
4776
99.9
2.52-2.71
X-RAY DIFFRACTION
4754
100
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi