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- PDB-1hcx: 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: 1hcx | ||||||
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Title | Choline binding domain of the major autolysin (C-LytA) from Streptococcus pneumoniae | ||||||
![]() | MAJOR 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: A Novel Solenoid Fold in the Cell Wall Anchoring Domain of the Pneumococcal Virulence Factor Lyta Authors: Fernandez-Tornero, C. / Lopez, R. / Garcia, E. / Gimenez-Gallego, G. / Romero, A. #1: Journal: Gene / Year: 1990 Title: Cloning and Expression of Gene Fragments Encoding the Choline-Binding Domain of Pneumococcal Murein Hydrolases Authors: Sanchez-Puelles, J.M. / Sanz, J.M. / Garcia, J.L. / Garcia, E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.4 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.58348, -0.21209, 0.78395), Vector: |
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Components
#1: Protein | Mass: 14949.556 Da / Num. of mol.: 2 / Fragment: CHOLINE-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase #2: Chemical | ChemComp-TPT / | #3: Chemical | ChemComp-CHT / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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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 / 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: Oct 30, 2000 / Details: TOROIDAL MIRROR | ||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→35 Å / Num. obs: 11378 / % possible obs: 99.7 % / Observed criterion σ(I): 8 / Redundancy: 4.5 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.049 / Net I/σ(I): 18 | ||||||||||||
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.266 / % possible all: 100 | ||||||||||||
Reflection | *PLUS Lowest resolution: 35 Å / Num. measured all: 105081 / Rmerge(I) obs: 0.049 | ||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.4388 Å2 / ksol: 0.318346 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→34.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 35 Å / % reflection Rfree: 10 % / Rfactor obs: 0.218 / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.218 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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