+
Open data
-
Basic information
Entry | Database: PDB / ID: 4gxq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of ATP bound RpMatB-BxBclM chimera B1 | ||||||
![]() | Malonyl CoA synthetase, Benzoate-CoA ligase Chimeric protein | ||||||
![]() | LIGASE / RpMatB-BxBclM chimera / ANL Superfamily / methylmalonate-CoA ligase / malonate-CoA ligase / methylmalonate / malonate | ||||||
Function / homology | ![]() benzoate-CoA ligase / benzoate-CoA ligase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / medium-chain fatty acid-CoA ligase activity / secondary metabolite biosynthetic process / fatty acid metabolic process / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rank, K.C. / Crosby, H.A. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
![]() | ![]() Title: Structural Insights into the Substrate Specificity of the Rhodopseudomonas palustris Protein Acetyltransferase RpPat: IDENTIFICATION OF A LOOP CRITICAL FOR RECOGNITION BY RpPat. Authors: Crosby, H.A. / Rank, K.C. / Rayment, I. / Escalante-Semerena, J.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 627.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 523.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 74.3 KB | Display | |
Data in CIF | ![]() | 108.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gxrC ![]() 4futS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 55892.242 Da / Num. of mol.: 3 Fragment: UNP Q6ND88 residues 1-443,466-506 and UNP Q13WK3 473-497 Mutation: K491A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CGA009, LB400 / Gene: matB, RPA0221 / Plasmid: PTEV5 / Production host: ![]() ![]() References: UniProt: Q6ND88, UniProt: Q13WK3, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.71 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES buffer (100 mM, pH 7.5), 200 mM potassium glutamate, polyethylene glycol 8000 (26 % (w/v), propylene glycol (5 %, w/v), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2012 |
Radiation | Monochromator: ROSENBAUM-ROCK HIGH-RESOLUTION DOUBLE-CRYSTAL MONOCHROMATOR. LN2 COOLED FIRST CRYSTAL, SAGITTAL FOCUSING 2ND CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 850800 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.8 / Num. unique all: 8163 / Rsym value: 0.436 / % possible all: 99.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4FUT Resolution: 2→24.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.872 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.609 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.95 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|