+Open data
-Basic information
Entry | Database: PDB / ID: 2x45 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Arg r 1 in complex with histamine | ||||||
Components | ALLERGEN ARG R 1 | ||||||
Keywords | ALLERGEN | ||||||
Function / homology | Function and homology information amine binding / symbiont-mediated perturbation of host defenses / extracellular region Similarity search - Function | ||||||
Biological species | ARGAS REFLEXUS (arthropod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Paesen, G.C. / Siebold, C. / Syme, N. / Harlos, K. / Graham, S.C. / Hilger, C. / Homans, S.W. / Hentges, F. / Stuart, D.I. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Allergen Arg R 1, a Histamine-Binding Lipocalin from a Soft Tick Authors: Paesen, G.C. / Siebold, C. / Syme, N. / Harlos, K. / Graham, S.C. / Hilger, C. / Homans, S.W. / Hentges, F. / Stuart, D.I. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2x45.cif.gz | 218.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2x45.ent.gz | 176.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x45_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2x45_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 2x45_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 2x45_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/2x45 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x45 | HTTPS FTP |
-Related structure data
Related structure data | 2x46SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
2 |
| ||||||||||||||||
3 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 15521.223 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARGAS REFLEXUS (arthropod) / Organ: SALIVARY GLAND / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI(DE3)PLYSS / References: UniProt: Q5GQ85 #2: Chemical | ChemComp-HSM / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.89 % / Description: NONE |
---|---|
Crystal grow | pH: 8.5 Details: 30% POLYETHYLENE GLYCOL 4000, 0.1 M TRIS.HCL, PH 8.5, 0.2 M SODIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 79040 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X46 Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.134 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.109 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|