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Yorodumi- PDB-6w80: Crystal structure of Glutamate-1-semialdehyde 2,1-aminomutase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w80 | ||||||
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Title | Crystal structure of Glutamate-1-semialdehyde 2,1-aminomutase from Stenotrophomonas maltophilia K279a in complex with PLP | ||||||
Components | Glutamate-1-semialdehyde 2,1-aminomutase | ||||||
Keywords | ISOMERASE / SSGCID / Stenotrophomonas maltophilia / Glutamate-1-semialdehyde 2 / 1-aminomutase / hemL / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information glutamate-1-semialdehyde 2,1-aminomutase / glutamate-1-semialdehyde 2,1-aminomutase activity / protoporphyrinogen IX biosynthetic process / transaminase activity / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Glutamate-1-semialdehyde 2,1-aminomutase from Stenotrophomonas maltophilia K279a in complex with PLP Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w80.cif.gz | 225.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w80.ent.gz | 147.5 KB | Display | PDB format |
PDBx/mmJSON format | 6w80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w80_validation.pdf.gz | 997.6 KB | Display | wwPDB validaton report |
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Full document | 6w80_full_validation.pdf.gz | 998.8 KB | Display | |
Data in XML | 6w80_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 6w80_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/6w80 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/6w80 | HTTPS FTP |
-Related structure data
Related structure data | 5i92S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 46141.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: hemL, Smlt3873 / Plasmid: StmaA.01026.c.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: B2FT35, glutamate-1-semialdehyde 2,1-aminomutase |
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#2: Chemical | ChemComp-PLP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.2 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 13.4 mg/mL StmaA.01026.c.B1.PW38743 + 2 mM PLP + 2 mM alanine against Molecular Dimensions Morpheus screen, condition g9 (10% w/V PEG20000, 20% V/V PEG550 MME, 20 mM sodium formate, 20 mM ...Details: 13.4 mg/mL StmaA.01026.c.B1.PW38743 + 2 mM PLP + 2 mM alanine against Molecular Dimensions Morpheus screen, condition g9 (10% w/V PEG20000, 20% V/V PEG550 MME, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium l-tartrate, 20 mM sodium oxamate, 100 mM Bicine/Trizma base, pH 8.5), direct cryoprotection, tray: 313929g9, puck jxa1-2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→50 Å / Num. obs: 79730 / % possible obs: 99.8 % / Redundancy: 10.338 % / Biso Wilson estimate: 23.293 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.062 / Χ2: 1.097 / Net I/σ(I): 20.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5i92 chain A as per MORDA Resolution: 1.4→34.47 Å / SU ML: 0.124 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.1634
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→34.47 Å
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Refine LS restraints |
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LS refinement shell |
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