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- PDB-1b2k: Structural effects of monovalent anions on polymorphic lysozyme c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1b2k | ||||||
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Title | Structural effects of monovalent anions on polymorphic lysozyme crystals | ||||||
![]() | PROTEIN (LYSOZYME) | ||||||
![]() | HYDROLASE / HYDROLASE (O-GLYCOSYL) | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vaney, M.C. / Broutin, I. / Ries-Kautt, M. / Ducruix, A. | ||||||
![]() | ![]() Title: Structural effects of monovalent anions on polymorphic lysozyme crystals. Authors: Vaney, M.C. / Broutin, I. / Retailleau, P. / Douangamath, A. / Lafont, S. / Hamiaux, C. / Prange, T. / Ducruix, A. / Ries-Kautt, M. #1: ![]() Title: Refinement of Triclinic Hen Egg-White Lysozyme at Atomic Resolution Authors: Walsh, M.A. / Schneider, T.R. / Sieker, L.C. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S. #2: ![]() Title: Structures of Monoclinic Lysozyme Iodide at 1.6 Ang. And of Triclinic Lysozyme Nitrate at 1.1 Ang Authors: Steinrauf, L.K. #3: ![]() Title: Locations of Bromide Ions in Tetragonal Lysozyme Crystals Authors: Lim, K. / Nadarajah, A. / Forsythe, E.L. / Pusey, M.L. #4: ![]() Title: High-Resolution Structure (1.33 Ang.) Of a Hewl Lysozyme Tetragonal Crystal Grown in the Apcf Apparatus. Data and Structural Comparison with a Crystal Grown Under Microgravity from Spachab-01 Mission Authors: Vaney, M.C. / Maignan, S. / Ries-Kautt, M. / Ducruix, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70 KB | Display | ![]() |
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PDB format | ![]() | 51.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1b0dC ![]() 1hf4C ![]() 1lcnC ![]() 193lS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-IOD / #3: Water | ChemComp-HOH / | Nonpolymer details | WATER MOLECULE HOH 746, WELL-DEFINED IN THE DENSITY, IS HYDROGEN-BONDED WITH NE OF ARG 112A WITH A ...WATER MOLECULE HOH 746, WELL-DEFINED IN THE DENSITY, IS HYDROGEN-BONDED WITH NE OF ARG 112A WITH A DISTANCE OF 3.45 ANG. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 33 % | ||||||||||||||||||
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Crystal grow | Temperature: 291 K / pH: 4.5 Details: THE ISOIONIC PROTEIN HEWL WAS ACIDIFIED BY ADDING OF HI UNTIL THE PH 4.5 WAS REACHED AT 291K WERE 25 MG/ML OF PROTEIN AND 0.07 M OF NAI VERSUS A WELL CONTAINING 0.14 M OF NAI AT PH4.5 | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: vapor diffusion, hanging dropDetails: pH is adjusted to 4.5 with HI, drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1992 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.901 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→13.3 Å / Num. obs: 26152 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.095 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.54 / % possible all: 95.6 |
Reflection | *PLUS Rmerge(I) obs: 0.095 |
Reflection shell | *PLUS % possible obs: 95.6 % / Rmerge(I) obs: 0.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 193L Resolution: 1.6→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 16.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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