[English] 日本語
Yorodumi- PDB-1a7l: DOMINANT B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a7l | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | DOMINANT B-CELL EPITOPE FROM THE PRES2 REGION OF HEPATITIS B VIRUS IN THE FORM OF AN INSERTED PEPTIDE SEGMENT IN MALTODEXTRIN-BINDING PROTEIN | |||||||||
Components | MALE-B363 | |||||||||
Keywords | TRANSPORT / PRES2 / EPITOPE / HEPATITIS B / MALTOSE-BINDING PROTEIN | |||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Saul, F.A. / Vulliez-Lenormand, B. / Lema, F. / Bentley, G.A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of a dominant B-cell epitope from the preS2 region of hepatitis B virus in the form of an inserted peptide segment in maltodextrin-binding protein. Authors: Saul, F.A. / Vulliez-le Normand, B. / Lema, F. / Bentley, G.A. #1: Journal: Protein Eng. / Year: 1997 Title: Maltodextrin-Binding Protein Hybrids Carrying Epitopes from the Pres2 Region of Hepatitis B Virus: Expression, Antibody-Binding and Preliminary Crystallographic Studies Authors: Vulliez-Le Normand, B. / Saul, F.A. / Martineau, P. / Lema, F. / Hofnung, M. / Bentley, G.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a7l.cif.gz | 220.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a7l.ent.gz | 178.5 KB | Display | PDB format |
PDBx/mmJSON format | 1a7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a7l_validation.pdf.gz | 534.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1a7l_full_validation.pdf.gz | 548.7 KB | Display | |
Data in XML | 1a7l_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 1a7l_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a7l ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a7l | HTTPS FTP |
-Related structure data
Related structure data | 1anfS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
4 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||
Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS THREE INDEPENDENT MOLECULES OF MALE-B363. EACH IS ASSOCIATED WITH A BOUND MOLECULE OF MALTOSE SUBSTRATE. THE FOLLOWING CHAIN IDENTIFIERS ARE USED: CHAIN A, MALE-B363 MOLECULE 1; CHAIN B, MALE-B363 MOLECULE 2; CHAIN C, MALE-B363 MOLECULE 3; CHAIN D, HET GROUP ASSOCIATED WITH MOLECULE 1; CHAIN E, HET GROUP ASSOCIATED WITH MOLECULE 2; CHAIN F, HET GROUP ASSOCIATED WITH MOLECULE 3; CHAIN X, SOLVENTS ASSOCIATED WITH MOLECULE 1; CHAIN Y, SOLVENTS ASSOCIATED WITH MOLECULE 2; CHAIN Z, SOLVENTS ASSOCIATED WITH MOLECULE 3. |
-Components
#1: Protein | Mass: 42650.176 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Strain: ED9 / Gene: MBP MUTANT / Plasmid: PPD91-(DERIVATIVE) / Gene (production host): MBP MUTANT / Production host: Escherichia coli (E. coli) / References: UniProt: P02928, UniProt: P0AEX9*PLUS #2: Polysaccharide | #3: Water | ChemComp-HOH / | Compound details | MALE-B363 IS AN INSERTION/DELETION MUTANT OF THE E. COLI MALTODEXTRIN-BINDING PROTEIN (MBP) ...MALE-B363 IS AN INSERTION/DELETION MUTANT OF THE E. COLI MALTODEXTR | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.5 Details: PROTEIN CONCENTRATION 3.0MG/ML, BUFFER 0.1M TRIS-HCL PH 8.5 WITH 0.2 M MGCL2, 1 MM MALTOSE, 26% PEG 4000. | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Vulliez-Le Normand, B., (1997) Protein Eng., 10, 175. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→15 Å / Num. obs: 24492 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.7 / % possible all: 90 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 15 Å / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 90 % / Redundancy: 3 % / Num. unique obs: 2146 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MBP RESIDUES 4 - 362 (PDB ENTRY 1ANF) Resolution: 2.9→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.03 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.357 / Rfactor Rwork: 0.248 |