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Yorodumi- PDB-4opm: Crystal structure of a putative lipase (lip1) from Acinetobacter ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4opm | ||||||
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Title | Crystal structure of a putative lipase (lip1) from Acinetobacter baumannii AYE at 1.70 A resolution | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / PF06342 family / DUF1057 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative lipase (lip1) from Acinetobacter baumannii AYE at 1.70 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 | 4opm.cif.gz | 268.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4opm.ent.gz | 219.9 KB | Display | PDB format |
PDBx/mmJSON format | 4opm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4opm_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4opm_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4opm_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 4opm_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/4opm ftp://data.pdbj.org/pub/pdb/validation_reports/op/4opm | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34282.750 Da / Num. of mol.: 2 / Fragment: UNP residues 26-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AYE / Gene: lip1, ABAYE2810 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: B0V9K7, triacylglycerol lipase |
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-Non-polymers , 5 types, 698 molecules
#2: Chemical | ChemComp-15P / | ||||||
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#3: Chemical | ChemComp-PE4 / #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE CONSTRUCT (26-330) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (26-330) 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: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.0500M lithium sulfate, 10.00% Glycerol, 30.00% polyethylene glycol 600, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97895,0.97963,0.91837 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→48.556 Å / Num. obs: 77844 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.011 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.81 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→48.556 Å / Cor.coef. Fo:Fc: 0.9653 / Cor.coef. Fo:Fc free: 0.9512 / Occupancy max: 1 / Occupancy min: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. 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 FOR THE REDUCED ...Details: 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. SULFATE(SO4), GLYCEROL(GOL) AND PEG FRAGMENTS (PE4 AND 15P) MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS. PGX IS LOCATED IN THE ACTIVE SITES.
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Displacement parameters | Biso max: 119.04 Å2 / Biso mean: 27.4117 Å2 / Biso min: 8.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.199 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→48.556 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 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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