[English] 日本語
Yorodumi- PDB-1dk0: CRYSTAL STRUCTURE OF THE HEMOPHORE HASA FROM SERRATIA MARCESCENS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dk0 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE HEMOPHORE HASA FROM SERRATIA MARCESCENS CRYSTAL FORM P2(1), PH8 | ||||||
Components | HEME-BINDING PROTEIN A | ||||||
Keywords | TRANSPORT PROTEIN / PROTEIN-HEME COMPLEX / TWO HEME INSERTIONS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.77 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 |
| ||||||
Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Biological assembly is a monomer. The other monomer in the AU probably does not have biological significance. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dk0.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dk0.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 1dk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dk0 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dk0 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | Biological assembly is a monomer. The other monomer in the AU probably does not have biological significance. |
-Components
#1: Protein | Mass: 19288.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q54450 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.72 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M NaHepes, pH8.0, 1.4M NaKTartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Details: Arnoux, P., (1999) Nat.Struct.Biol., 6, 516. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→20 Å / Num. all: 31089 / Num. obs: 31089 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.77→1.82 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.371 / % possible all: 89.3 |
Reflection shell | *PLUS % possible obs: 89.3 % / Mean I/σ(I) obs: 2 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.77→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→15 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
|