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Yorodumi- PDB-1im0: OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI N156A ACTIVE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1im0 | ||||||
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Title | OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI N156A ACTIVE SITE MUTANT PH 8.3 | ||||||
Components | OUTER MEMBRANE PHSOPHOLIPASE A | ||||||
Keywords | HYDROLASE / MEMBRANE PROTEIN / ANTI-PARALLEL BETA BARREL / MEMBRANE PHOSPHOLIPASE / SERINE HYDROLASE / CATALYTIC TRIAD | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Snijder, H.J. / Van Eerde, J.H. / Kingma, R.L. / Kalk, K.H. / Dekker, N. / Egmond, M.R. / Dijkstra, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad. Authors: Snijder, H.J. / Van Eerde, J.H. / 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. / Verheij, H.M. / Kalk, K.H. / Dijkstra, B.W. | ||||||
History |
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Remark 600 | HETEROGEN ATOMS C3'-C8' OF BOG 502 HAVE MISSING ELECTRON DENSITY. ATOMS C5'-C8' OF BOG 504, 505 ...HETEROGEN ATOMS C3'-C8' OF BOG 502 HAVE MISSING ELECTRON DENSITY. ATOMS C5'-C8' OF BOG 504, 505 LACK INTERPRETABLE ELECTRON DENSITY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1im0.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1im0.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 1im0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1im0_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1im0_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1im0_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1im0_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/1im0 ftp://data.pdbj.org/pub/pdb/validation_reports/im/1im0 | HTTPS FTP |
-Related structure data
Related structure data | 1ildC 1ilzC 1qd5S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 31493.852 Da / Num. of mol.: 1 / Mutation: N156A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A921, phospholipase A1 | ||||
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#2: Sugar | ChemComp-BOG / #3: Chemical | #4: 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: 2.86 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: MPD, calcium chloride, bis-tris buffer pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS + NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→21 Å / Num. obs: 106289 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.98→3.03 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 7.9 / Num. unique all: 372 / Rsym value: 0.34 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 21 Å / Num. obs: 7686 / Num. measured all: 106289 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 372 / Rmerge(I) obs: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QD5 WITH ACTIVE SITE RESIDUES TRUNCATED TO ALA. ALL WATER AND DETERGENT MOLECULES REMOVED. ALL ATOMS WERE GIVEN A RANDOM SHIFT OF ALMOST 0.5 ANGSTROM. Resolution: 2.98→21 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT CORRECTION APPLIED bulk solvent: density level= 0.439543 e/A^3 B-factor= 81.1117 A^2
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.98→21 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 21 Å / σ(F): 0 / Rfactor obs: 0.226 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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