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Yorodumi- PDB-1qj3: Crystal structure of 7,8-diaminopelargonic acid synthase in compl... -
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-Basic information
Entry | Database: PDB / ID: 1qj3 | ||||||
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Title | Crystal structure of 7,8-diaminopelargonic acid synthase in complex with 7-keto-8-aminopelargonic acid | ||||||
Components | 7,8-DIAMINOPELARGONIC ACID SYNTHASE | ||||||
Keywords | TRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / BIOTIN BIOSYNTHESIS | ||||||
Function / homology | Function and homology information adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / dethiobiotin synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.7 Å | ||||||
Authors | Kaeck, H. / Sandmark, J. / Gibson, K.J. / Lindqvist, Y. / Schneider, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal Structure of Diaminopelargonic Acid Synthase; Evolutionary Relationships between Pyridoxal-5'-Phosphate Dependent Enzymes Authors: Kack, H. / Sandmark, J. / Gibson, K.J. / Schneider, G. / Lindqvist, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qj3.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qj3.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qj3_validation.pdf.gz | 408.6 KB | Display | wwPDB validaton report |
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Full document | 1qj3_full_validation.pdf.gz | 434.4 KB | Display | |
Data in XML | 1qj3_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 1qj3_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/1qj3 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/1qj3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99995, 0.01019, 0.0007), Vector: |
-Components
#1: Protein | Mass: 47310.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Cellular location: CYTOPLASM / Gene: BIOA / Plasmid: PET24 / Cellular location (production host): CYTOPLASM / Gene (production host): BIOA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P12995, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | PYRIDOXAL-5'-PHOSPHATE IS BOUND TO LYS 274 IN BOTH CHAINS | Sequence details | FROM THE ELECTRON DENSITY TRP14 IS REINTERPRE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 30 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 25% PEG-4000, 20% MPD, 100MM HEPES PH7.5, 5MM KAPA (7-KETO-8-AMINOPELARGONIC ACID), 20 DEGREES C, MICROSEEDING., pH 7.50 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.3 / Method: vapor diffusionDetails: drop consists of equal volume of protein and precipitant solutions | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 21479 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 42.6 Å2 / Rsym value: 0.104 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.7→2.82 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.326 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 124908 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.326 |
-Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: DUE TO DISORDERED MAINCHAIN THE FOLLOWING RESIDUES WERE REMOVED FROM THE MODEL OF CHAIN A: SER 160, MET 161, HIS 162, SER 163, LEU 164, TRP 165, LYS 166, GLY 167, TYR 168, ASP 183, GLY 300, ...Details: DUE TO DISORDERED MAINCHAIN THE FOLLOWING RESIDUES WERE REMOVED FROM THE MODEL OF CHAIN A: SER 160, MET 161, HIS 162, SER 163, LEU 164, TRP 165, LYS 166, GLY 167, TYR 168, ASP 183, GLY 300, ALA 301, GLN 429 DUE TO DISORDERED MAINCHAIN THE FOLLOWING RESIDUES WERE REMOVED FROM THE MODEL OF CHAIN B: SER 160, MET 161, HIS 162, SER 163, LEU 164, TRP 165, LYS 166, GLY 167, TYR 168, ASP 183, GLY 184, GLY 300, ALA 301, GLN 429
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Displacement parameters | Biso mean: 51.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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