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- PDB-1sjd: x-ray structure of o-succinylbenzoate synthase complexed with n-s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1sjd | ||||||
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Title | x-ray structure of o-succinylbenzoate synthase complexed with n-succinyl phenylglycine | ||||||
![]() | N-acylamino acid racemase | ||||||
![]() | LYASE / ISOMERASE / racemase | ||||||
Function / homology | ![]() o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / menaquinone biosynthetic process / isomerase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thoden, J.B. / Taylor-Ringia, E.A. / Garrett, J.B. / Gerlt, J.A. / Holden, H.M. / Rayment, I. | ||||||
![]() | ![]() Title: Evolution of Enzymatic Activity in the Enolase Superfamily: Structural Studies of the Promiscuous o-Succinylbenzoate Synthase from Amycolatopsis Authors: Thoden, J.B. / Taylor-Ringia, E.A. / Garrett, J.B. / Gerlt, J.A. / Holden, H.M. / Rayment, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 311.2 KB | Display | ![]() |
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PDB format | ![]() | 250.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 77.1 KB | Display | |
Data in CIF | ![]() | 108.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sjaC ![]() 1sjbSC ![]() 1sjcC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39448.270 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NPG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.16 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 8 Details: PEG 8000, HEPES, MgCl2, n-succinylphenylglycine, pH 8.0, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Apr 7, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6525 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. all: 186822 / Num. obs: 186822 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rsym value: 0.085 / Net I/σ(I): 40.1 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.377 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1sjb Resolution: 1.87→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.87→50 Å
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Refine LS restraints |
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