[English] 日本語
![](img/lk-miru.gif)
- PDB-3mqd: Crystal structure of beta-ketoacyl synthase from brucella meliten... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3mqd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of beta-ketoacyl synthase from brucella melitensis with FOL 0758, (1-methyl-1h-indazol-3-yl) methanol | ||||||
![]() | Beta-ketoacyl synthase | ||||||
![]() | TRANSFERASE / SSGCID / ALS COLLABORATIVE CRYSTALLOGRAPHY / BETA-KETOACYL SYNTHASE / BRUCELLA MELITENSIS / FRAGMENTS OF LIFE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Structural characterization of beta-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites. Authors: Patterson, E.I. / Nanson, J.D. / Abendroth, J. / Bryan, C. / Sankaran, B. / Myler, P.J. / Forwood, J.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 188.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 146.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 451.2 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lrfSC ![]() 3u0eC ![]() 3u0fC ![]() 4jv3C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | BIOMOLECULE: NULL SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. REMARK: BIOLOGICAL UNIT IS A DIMER |
-
Components
#1: Protein | Mass: 45643.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ABORTUS 2308 / Gene: fabB, BAB1_2173 / Plasmid: AVA0421 / Production host: ![]() ![]() References: UniProt: Q2YQQ9, glucosamine-phosphate N-acetyltransferase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-3MQ / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.29 % |
---|---|
Crystal grow | Temperature: 290 K / pH: 8.5 Details: MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE; CRYSTAL SOAKED 100MM MES PH 6.5, 250MM NACL, 30% PEG 3350, 10% GLYCEROL; BRABA.00113.A AT 22.9MG/ML, VAPOR ...Details: MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE; CRYSTAL SOAKED 100MM MES PH 6.5, 250MM NACL, 30% PEG 3350, 10% GLYCEROL; BRABA.00113.A AT 22.9MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM Q315R / Detector: CCD / Date: Apr 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→4181 Å / Num. obs: 111226 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.34 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.07 |
Reflection shell | Resolution: 1.25→1.28 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4 / % possible all: 99.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: native structure, 3LRF Resolution: 1.25→41.81 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.821 / SU ML: 0.017 Isotropic thermal model: anisotropic, some solvent atoms left isotropic Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.42 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→41.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.25→1.28 Å / Total num. of bins used: 20
|