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Yorodumi- PDB-1cqx: Crystal structure of the flavohemoglobin from Alcaligenes eutroph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cqx | ||||||
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Title | Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution | ||||||
Components | FLAVOHEMOPROTEIN | ||||||
Keywords | LIPID BINDING PROTEIN / GLOBIN FOLD / SIX-STRANDED ANTIPARALLEL BETA SHEET / HELIX-FLANKED FIVE-STRANDED PARALLEL BETA SHEET | ||||||
Function / homology | Function and homology information nitric oxide dioxygenase / nitric oxide dioxygenase NAD(P)H activity / response to nitrosative stress / FAD binding / oxygen carrier activity / response to toxic substance / oxygen binding / heme binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Cupriavidus necator (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å | ||||||
Authors | Ermler, U. / Siddiqui, R.A. / Cramm, R. / Friedrich, B. | ||||||
Citation | Journal: EMBO J. / Year: 1995 Title: Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution. Authors: Ermler, U. / Siddiqui, R.A. / Cramm, R. / Friedrich, B. #1: Journal: Eur.J.Biochem. / Year: 1999 Title: Phospholipid bound to the flavohemoprotein from alcaligenes eutrophus Authors: Ollesch, G. / Kaunzinger, A. / Juchelka, D. / Schubert-Zsilavecz, M. / Ermler, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cqx.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cqx.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 1cqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/1cqx ftp://data.pdbj.org/pub/pdb/validation_reports/cq/1cqx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44845.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cupriavidus necator (bacteria) Keywords: COMPLEXED WITH HEME, FLAVIN-ADENINE DINUCLEOTIDE AND PHOSPHO LIPID References: UniProt: P39662 |
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-Non-polymers , 5 types, 588 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.07 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: protein solution: TRIS, potassium chloride, DTT, plus precipitant; precipitant: PEG 3350, sodium chloride, sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 281K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 196672 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.151 / Num. unique all: 8118 / % possible all: 62.7 |
Reflection shell | *PLUS % possible obs: 62.7 % |
-Processing
Software |
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Refinement | Resolution: 1.75→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 29433623.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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