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- PDB-1h8g: C-terminal domain of the major autolysin (C-LytA) from Streptococ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h8g | ||||||
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Title | C-terminal 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. / Garcia, E. / Lopez, R. / 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 | ![]() | 49.2 KB | Display | ![]() |
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PDB format | ![]() | 39.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.8 KB | Display | ![]() |
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Full document | ![]() | 452.7 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.75571, -0.19738, -0.62446), Vector: Details | THE CHOLINE-BINDING DOMAIN FRAGMENT CRYSTALLISES AS ATETRAMERIC ASSEMBLY FORMING A CYCLIC DOUGHNUT STRUCTURE. | |
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Components
#1: Protein | Mass: 11153.843 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-CHT / #3: Water | ChemComp-HOH / | |
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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 % Description: A FIRST STRUCTURE, WHOSE STATISTICS HAVE NOT BEEN SUBMITTED, WAS DETERMINED TO 3.0 ANGSTROM RESOLUTION THROUGH A MAD EXPERIMENT. A SECOND EXPERIMENT WAS THEN PERFORMED ON A SINGLE ...Description: A FIRST STRUCTURE, WHOSE STATISTICS HAVE NOT BEEN SUBMITTED, WAS DETERMINED TO 3.0 ANGSTROM RESOLUTION THROUGH A MAD EXPERIMENT. A SECOND EXPERIMENT WAS THEN PERFORMED ON A SINGLE CRYSTAL. IT IS STRUCTURE REFINED AGAINST THE DATA FROM THIS SECOND EXPERIMENT THAT IS PRESENTED IN THIS ENTRY | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 30% MPD, 0.2 M NACL, 0.1 M NA-ACETATE, PH 4.6, 0.2 M GUANIDINE-HCL, 0.15 M CHOLINE-CL. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: GE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9073 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 12997 / % possible obs: 97.8 % / Observed criterion σ(I): 8 / Redundancy: 3 % / Biso Wilson estimate: 46.3 Å2 / Rsym value: 0.048 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.368 / % possible all: 97.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 13018 / Num. measured all: 117161 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 97.9 % / Rmerge(I) obs: 0.368 |
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Processing
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Refinement | Method to determine structure: ![]() Details: SEVERAL CYCLES WITH CNS, ONE SHELX CYCLE TO FIND WATER MOLECULES, FINAL CYCLE WITH CNS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.6129 Å2 / ksol: 0.344715 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→32.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / % reflection Rfree: 8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.53 Å |