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- PDB-1gvm: CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gvm | ||||||
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Title | CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE | ||||||
![]() | AUTOLYSIN | ||||||
![]() | CHOLINE-BINDING DOMAIN / CELL WALL ATTACHMENT | ||||||
Function / homology | ![]() N-acetylmuramoyl-L-alanine amidase / establishment of competence for transformation / N-acetylmuramoyl-L-alanine amidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan catabolic process / cell wall organization / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, A. | ||||||
![]() | ![]() Title: Two New Crystal Forms of the Choline-Binding Domain of the Major Pneumococcal Autolysin: Insights Into the Dynamics of the Active Dimeric Authors: Fernandez-Tornero, C. / Garcia, E. / Lopez, R. / Gimenez-Gallego, G. / Romero, A. #1: ![]() Title: A Novel Solenoid Fold in the Cell Wall Anchoring Domain of the Pneumococcal Virulence Factorlyta Authors: Fernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, 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 | ![]() | 172.3 KB | Display | ![]() |
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PDB format | ![]() | 139.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 511.5 KB | Display | ![]() |
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Full document | ![]() | 548.9 KB | Display | |
Data in XML | ![]() | 35.8 KB | Display | |
Data in CIF | ![]() | 46.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hcxS S: Starting model for refinement |
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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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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 15876.638 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase #2: Chemical | ChemComp-CHT / #3: Chemical | ChemComp-DDQ / | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | Sequence details | ALA D 194, DISORDERED SIDE-CHAIN IN PDB ENTRY. THE FIRST THREE RESIDUES OF EACH CHAIN (GLY185, ...ALA D 194, DISORDERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.4 Details: 30% PEG 4000, 0.2 M NA-ACETATE, 0.1 M AMMONIUM-ACETATE, PH 6.4, 0.15 M CHOLINE-CL, 0.4 MM DDAO. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / pH: 6.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 15, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→33 Å / Num. obs: 23628 / % possible obs: 98.5 % / Observed criterion σ(I): 8 / Redundancy: 3.2 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7 |
Reflection | *PLUS Lowest resolution: 33 Å / Num. measured all: 74838 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / % possible obs: 98.7 % / Rmerge(I) obs: 0.28 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HCX Resolution: 2.8→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 740335.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.0206 Å2 / ksol: 0.436606 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2.8 Å / % reflection Rfree: 8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.95 Å |