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Yorodumi- PDB-2pma: Structural Genomics, the crystal structure of a protein Lpg0085 w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pma | ||||||
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Title | Structural Genomics, the crystal structure of a protein Lpg0085 with unknown function (DUF785) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1. | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC86035.2 / protein Lpg0085 / DUF785 / Legionella pneumophila subsp. pneumophila str. Philadelphia 1 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Putative ATP-dependant zinc protease / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta / ACETATE ION / FORMIC ACID / Uncharacterized protein Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å | ||||||
Authors | Tan, K. / Mulligan, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a protein Lpg0085 with unknown function (DUF785) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1. Authors: Tan, K. / Mulligan, R. / Moy, S. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. THE ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pma.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pma.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pma_validation.pdf.gz | 462.8 KB | Display | wwPDB validaton report |
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Full document | 2pma_full_validation.pdf.gz | 467.1 KB | Display | |
Data in XML | 2pma_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 2pma_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/2pma ftp://data.pdbj.org/pub/pdb/validation_reports/pm/2pma | 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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Unit cell |
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Details | Experimentally unknown. It could be monomeric based on molecular packing |
-Components
#1: Protein | Mass: 16178.821 Da / Num. of mol.: 2 / Fragment: Residues 26-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Species: Legionella pneumophila / Strain: Philadelphia 1, DSM 7513 / Gene: lpg0085 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5ZZC6 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG1000, 0.2M MgCl2, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.89→37.77 Å / Num. all: 27464 / Num. obs: 27464 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 52.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 8.2 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.89→37.77 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.726 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 35.063 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→37.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.942 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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