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Yorodumi- PDB-3dzz: CRYSTAL STRUCTURE OF A PUTATIVE PLP-DEPENDENT AMINOTRANSFERASE (L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dzz | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE PLP-DEPENDENT AMINOTRANSFERASE (LBUL_1103) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.61 A RESOLUTION | ||||||
Components | putative pyridoxal 5'-phosphate-dependent C-S lyase | ||||||
Keywords | TRANSFERASE / PUTATIVE PLP-DEPENDENT AMINOTRANSFERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | Function and homology information Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.61 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative pyridoxal 5'-phosphate-dependent C-S lyase (YP_813084.1) from LACTOBACILLUS DELBRUECKII BULGARICUS ATCC BAA-365 at 1.61 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dzz.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dzz.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 3dzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/3dzz ftp://data.pdbj.org/pub/pdb/validation_reports/dz/3dzz | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44844.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 (bacteria) Gene: YP_813084.1, LBUL_1103 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q04A76 |
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-Non-polymers , 6 types, 587 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-PG4 / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
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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: 40.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M calcium acetate, 40.0% polyethylene glycol 300, 0.1M sodium cacodylate pH 6.5, Additive - 0.001M pyridoxal 5'-phosphate (PLP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K, NANODROP' |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 16, 2008 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.61→38.778 Å / Num. obs: 93024 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.71 % / Biso Wilson estimate: 18.602 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.47 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.61→38.778 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.994 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.08 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.CA IONS, ACETATE IONS AND PEG MOLECULES FROM CRYSTALLIZATION CONDITIONS ARE MODELED INTO THE STRUCTURE. 5.PLP MOLECULE AS ADDITIVE FROM CRYSTALLIZATION WAS MODELED IN THE CONSERVED ACTIVE SITE OF EACH SUBUNIT ACCORDING TO THIS PROTEIN'S SEQUENCE BASED FUNCTION PREDICITION. THE PLP MOLECULE AND LYS 233 FORMED A SCHIFF BASE, WHICH IS REFINED AS THE COVALENT COMPOUND LLP.
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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: 16.011 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→38.778 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.652 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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