+Open data
-Basic information
Entry | Database: PDB / ID: 3g7x | ||||||
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Title | Female-specific histamine-binding protein 2, D24R mutant | ||||||
Components | Female-specific histamine-binding protein 2 | ||||||
Keywords | IMMUNE SYSTEM / lipocalin / beta barrel | ||||||
Function / homology | Function and homology information amine binding / symbiont-mediated perturbation of host defenses / extracellular region Similarity search - Function | ||||||
Biological species | Rhipicephalus appendiculatus (arthropod) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Dennis, C.A. / Homans, S.W. | ||||||
Citation | Journal: To be Published Title: Entropic contributions to binding in a 'Hydrophilic' Ligand-Protein Interaction Authors: Syme, N.R. / Dennis, C.A. / Bronowska, A. / Paesen, G. / Homans, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g7x.cif.gz | 166.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g7x.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 3g7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/3g7x ftp://data.pdbj.org/pub/pdb/validation_reports/g7/3g7x | HTTPS FTP |
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-Related structure data
Related structure data | 3gaqC 1qftS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19526.152 Da / Num. of mol.: 2 / Mutation: D24R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhipicephalus appendiculatus (arthropod) Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O77421 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: protein at 10 mg/ml containing 2 mM Histamine, Reservoir contained 2.6 M Ammonium Sulphate, 0.1 M Bicine, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2008 |
Radiation | Monochromator: Si111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→55.3 Å / Num. all: 65264 / Num. obs: 65264 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 21.068 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / Num. unique all: 9456 / Rsym value: 0.544 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1QFT Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.905 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.107 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.989 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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