+Open data
-Basic information
Entry | Database: PDB / ID: 2al0 | ||||||
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Title | Crystal structure of nitrophorin 2 ferrous aqua complex | ||||||
Components | Nitrophorin 2 | ||||||
Keywords | TRANSPORT PROTEIN / beta barrel / lipocalin / ferrous heme | ||||||
Function / homology | Function and homology information histamine binding / nitric oxide binding / vasodilation / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Weichsel, A. / Berry, R.E. / Walker, F.A. / Montfort, W.R. | ||||||
Citation | Journal: To be Published Title: Crystal structures, ligand induced conformational change and heme deformation in complexes of nitrophorin 2, a nitric oxide transport protein from rhodnius prolixus Authors: Weichsel, A. / Berry, R.E. / Walker, F.A. / Montfort, W.R. #1: Journal: J.Biol.Chem. / Year: 2000 Title: The crystal structure of nitrophorin 2 Authors: Andersen, J.F. / Montfort, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2al0.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2al0.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 2al0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2al0_validation.pdf.gz | 827.4 KB | Display | wwPDB validaton report |
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Full document | 2al0_full_validation.pdf.gz | 830.4 KB | Display | |
Data in XML | 2al0_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 2al0_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/2al0 ftp://data.pdbj.org/pub/pdb/validation_reports/al/2al0 | HTTPS FTP |
-Related structure data
Related structure data | 2acpC 2ah7C 2allC 2ammC 2asnC 2eu7C 2gtfC 1peeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20080.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q26241 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-CIT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.65 Å3/Da / Density % sol: 24.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2004 / Details: bent Si-mirror |
Radiation | Monochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→23 Å / Num. all: 21168 / Num. obs: 21168 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.05 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2039 / Rsym value: 0.23 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1PEE Resolution: 1.6→23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.832 / SU ML: 0.066 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.108 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.075 Å2
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Refine analyze | Luzzati coordinate error obs: 0.182 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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