+Open data
-Basic information
Entry | Database: PDB / ID: 1fw2 | ||||||
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Title | OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI | ||||||
Components | OUTER MEMBRANE PHOSPHOLIPASE A | ||||||
Keywords | hydrolase / membrane protein / ANTI-PARALLEL BETA BARREL DIMER | ||||||
Function / homology | Function and homology information phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / phospholipase activity / phosphatidylglycerol metabolic process / lysophospholipase activity / phospholipase A2 activity / phospholipase A2 / lipid catabolic process ...phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / phospholipase activity / phosphatidylglycerol metabolic process / lysophospholipase activity / phospholipase A2 activity / phospholipase A2 / lipid catabolic process / cell outer membrane / calcium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Snijder, H.J. / Kingma, R.L. / Kalk, K.H. / Dekker, N. / Egmond, M.R. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli. Authors: Snijder, H.J. / Kingma, R.L. / Kalk, K.H. / Dekker, N. / Egmond, M.R. / Dijkstra, B.W. #1: Journal: Nature / Year: 1999 Title: Structural Evidence for Dimerization-Regulated Activation of an Integral Membrane Phospholipase Authors: Snijder, H.J. / Ubarretxena-Belandia, I. / Blaauw, M. / Kalk, K.H. / Verheij, H.M. / Egmond, M.R. / Dekker, N. / Dijkstra, B.W. #2: Journal: FEBS Lett. / Year: 1995 Title: Crystallization and Preliminary X-Ray Analysis of Outer Membrane Phospholipase a from Escherichia Coli Authors: Blaauw, M. / Dekker, N. / Kalk, K.H. / Verheij, H.M. / Dijkstra, B.W. #3: Journal: Biochim.Biophys.Acta / Year: 2000 Title: Bacterial phospholipase A: structure and function of an integral membrane phospholipase Authors: Snijder, H.J. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fw2.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fw2.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1fw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fw2_validation.pdf.gz | 367.1 KB | Display | wwPDB validaton report |
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Full document | 1fw2_full_validation.pdf.gz | 371.9 KB | Display | |
Data in XML | 1fw2_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 1fw2_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/1fw2 ftp://data.pdbj.org/pub/pdb/validation_reports/fw/1fw2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31536.875 Da / Num. of mol.: 1 / Fragment: OMPLA WITH N-TERMINAL EXTENSION / Mutation: ARIRAP EXTENSION Source method: isolated from a genetically manipulated source Details: COVALENTLY SULFONYLATED ON SERINE144 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A921, phospholipase A1 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.51 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: MPD, calcium chloride, Bis-Tris, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Details: Blaauw, M., (1995) FEBS Lett., 373, 10. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 9975 / Num. obs: 9975 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.084 / % possible all: 62.3 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 47201 |
Reflection shell | *PLUS % possible obs: 62.3 % / Mean I/σ(I) obs: 10.3 |
-Processing
Software |
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Refinement | Resolution: 2.6→30 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: anisotropic scaling and bulk solvent correction applied
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Displacement parameters | Biso mean: 49.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 10
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.385 / % reflection Rfree: 8.1 % / Rfactor Rwork: 0.336 / Rfactor obs: 0.336 |