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Open data
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Basic information
Entry | Database: PDB / ID: 1qd6 | ||||||
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Title | OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI | ||||||
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![]() | MEMBRANE PROTEIN / ANTI-PARALLEL BETA BARREL DIMER | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Snijder, H.J. / Ubarretxena-Belandia, I. / Blaauw, M. / Kalk, K.H. / Verheij, H.M. / Egmond, M.R. / Dekker, N. / Dijkstra, B.W. | ||||||
![]() | ![]() 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. #1: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.8 KB | Display | ![]() |
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PDB format | ![]() | 89.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.7 KB | Display | ![]() |
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Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qd5SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Details | The biological assembly is a dimer constructed from chain A,C and B,D related by a NCS twofold rotation |
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Components
#1: Protein/peptide | Mass: 1402.640 Da / Num. of mol.: 2 / Fragment: RESDIUES 33-45 / Source method: obtained synthetically / References: UniProt: P0A921 #2: Protein | Mass: 27713.598 Da / Num. of mol.: 2 Mutation: ENZYME WITH N-TERMINAL EXTENSION ARIRAP AND COVALENTLY SULFONYLATED ON SERINE144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE N-TERMINAL WAS MUTATED TO EXTEND WITH RESIDUES ARIRAP | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.28 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: PEG400, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusionDetails: protein solution is mixed in a 3:2 ratio with well solution | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 13, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99385 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20.3 Å / Num. all: 76223 / Num. obs: 28336 / % possible obs: 74.1 % / Redundancy: 2.69 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.1→2.17 Å / Rmerge(I) obs: 0.265 / Num. unique all: 2510 / % possible all: 66.7 |
Reflection shell | *PLUS % possible obs: 66.7 % |
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Processing
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Refinement | Starting model: MONOMER OMPLA (1QD5) WITHOUT WATER/DETERGENT MOLECULES Resolution: 2.1→20.3 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent correction Anisotropic scaling
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Displacement parameters | Biso mean: 34.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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