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Yorodumi- PDB-1x8q: 0.85 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x8q | ||||||
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Title | 0.85 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus in Complex with Water at pH 5.6 | ||||||
Components | Nitrophorin 4 | ||||||
Keywords | LIGAND BINDING PROTEIN / Lipocalin / beta barrel / ferric heme | ||||||
Function / homology | Function and homology information nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodnius prolixus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.85 Å | ||||||
Authors | Kondrashov, D.A. / Roberts, S.A. / Weichsel, A. / Montfort, W.R. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Protein functional cycle viewed at atomic resolution: conformational change and mobility in nitrophorin 4 as a function of pH and NO binding Authors: Kondrashov, D.A. / Roberts, S.A. / Weichsel, A. / 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 | 1x8q.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x8q.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 1x8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x8q_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1x8q_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1x8q_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1x8q_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/1x8q ftp://data.pdbj.org/pub/pdb/validation_reports/x8/1x8q | HTTPS FTP |
-Related structure data
Related structure data | 1x8nC 1x8oC 1x8pC 1d2uS 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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Details | The biological assembly is a monomer consisting of chain A and the heme, and can be generated by the identity operation: x,y,z |
-Components
#1: Protein | Mass: 20292.664 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: Q94734 |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 1.63 Å3/Da / Density % sol: 24.3 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K |
-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 4 / Detector: CCD / Date: Aug 24, 2002 / Details: Bent conical Si-mirror (Rh coating) |
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: 0.85→22 Å / Num. all: 113651 / Num. obs: 113651 / % possible obs: 80.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 0.85→0.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8407 / Rsym value: 0.23 / % possible all: 63.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1D2U Resolution: 0.85→6 Å / Num. parameters: 18103 / Num. restraintsaints: 19193 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.9%. Hydrogens were added in calculated positions, further reducing free R by 1%.
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Displacement parameters | Biso mean: 12.1 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.097 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 103 / Occupancy sum hydrogen: 1394.2 / Occupancy sum non hydrogen: 1802.79 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→6 Å
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Refine LS restraints |
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