[English] 日本語
Yorodumi- PDB-1h8g: C-terminal domain of the major autolysin (C-LytA) from Streptococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h8g | ||||||
---|---|---|---|---|---|---|---|
Title | C-terminal domain of the major autolysin (C-LytA) from Streptococcus pneumoniae | ||||||
Components | MAJOR AUTOLYSIN | ||||||
Keywords | CHOLINE-BINDING DOMAIN / CELL WALL ATTACHMENT | ||||||
Function / homology | Function and homology information 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 | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Fernandez-Tornero, C. / Garcia, E. / Lopez, R. / Gimenez-Gallego, G. / Romero, A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 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 |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1h8g.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1h8g.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 1h8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h8g_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1h8g_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 1h8g_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1h8g_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8g ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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. | |
-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.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Cellular location: EXTRACELLULAR / Gene: LYTA / Plasmid: PCE17 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P06653, N-acetylmuramoyl-L-alanine amidase #2: Chemical | ChemComp-CHT / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9073 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.4→32.31 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1544106.38 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: SEVERAL CYCLES WITH CNS, ONE SHELX CYCLE TO FIND WATER MOLECULES, FINAL CYCLE WITH CNS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.6129 Å2 / ksol: 0.344715 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→32.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / % reflection Rfree: 8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 2.53 Å |