+Open data
-Basic information
Entry | Database: PDB / ID: 1dkh | ||||||
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Title | CRYSTAL STRUCTURE OF THE HEMOPHORE HASA, PH 6.5 | ||||||
Components | HEME-BINDING PROTEIN A | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.2 Å | ||||||
Authors | Arnoux, P. / Haser, R. / Izadi-Pruneyre, N. / Lecroisey, A. / Czjzek, M. | ||||||
Citation | Journal: Proteins / Year: 2000 Title: Functional aspects of the heme bound hemophore HasA by structural analysis of various crystal forms. Authors: Arnoux, P. / Haser, R. / Izadi-Pruneyre, N. / Lecroisey, A. / Czjzek, M. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: The Crystal Structure of HasA, a Hemophore Secreted by Serratia marcescens Authors: Arnoux, P. / Haser, R. / Izadi, N. / Lecroisey, A. / Delepierre, M. / Wandersman, C. / Czjzek, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dkh.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dkh.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dkh_validation.pdf.gz | 745.2 KB | Display | wwPDB validaton report |
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Full document | 1dkh_full_validation.pdf.gz | 761.1 KB | Display | |
Data in XML | 1dkh_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 1dkh_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dkh ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dkh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer. |
-Components
#1: Protein | Mass: 19288.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q54450 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-SM / | #4: Chemical | ChemComp-HEM / | #5: Water | ChemComp-HOH / | Compound details | LOW RESOLUTION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.92 Å3/Da / Density % sol: 75.02 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Cacodylate buffer pH6.5, Zinc Acetate 140mM, Glycerol 2%, PEG8000 10%, Samarium Chloride 10mM., VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Arnoux, P., (1999) Nat.Struct.Biol., 6, 516. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 29, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→12 Å / Num. all: 6285 / Num. obs: 6229 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.291 / Num. unique all: 647 / % possible all: 99.7 |
Reflection shell | *PLUS % possible obs: 99.7 % |
-Processing
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Refinement | Resolution: 3.2→12 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.2→12 Å
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Refine LS restraints |
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