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- PDB-1i4y: THE CRYSTAL STRUCTURE OF PHASCOLOPSIS GOULDII WILD TYPE METHEMERYTHRIN -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i4y | ||||||
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Title | THE CRYSTAL STRUCTURE OF PHASCOLOPSIS GOULDII WILD TYPE METHEMERYTHRIN | ||||||
![]() | METHEMERYTHRIN | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / hemerythrin / oxygen binding / diiron / four-helix bundle / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Farmer, C.S. / Kurtz Jr., D.M. / Liu, Z.-J. / Wang, B.C. / Rose, J. | ||||||
![]() | ![]() Title: The crystal structures of Phascolopsis gouldii wild type and L98Y methemerythrins: structural and functional alterations of the O2 binding pocket. Authors: Farmer, C.S. / Kurtz Jr., D.M. / Liu, Z.J. / Wang, B.C. / Rose, J. / Ai, J. / Sanders-Loehr, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.9 KB | Display | ![]() |
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PDB format | ![]() | 164.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.8 KB | Display | ![]() |
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Full document | ![]() | 435.1 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i4zC ![]() 2hmqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13626.386 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-FEO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.63 % | ||||||||||||||||||||
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Crystal grow | Temperature: 281.65 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Glycerol, HEPES, sodium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.65K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 2000 / Detector: CCD / Date: Apr 8, 1998 / Details: Gobel Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→72.12 Å / Num. all: 88489 / Num. obs: 78659 / % possible obs: 83 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 1.47 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 6.56 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 1.38 % / Rmerge(I) obs: 0.315 / Num. unique all: 9788 / % possible all: 62.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HMQ Resolution: 1.8→72.12 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 39907.1 / 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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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.4492 Å2 / ksol: 0.397062 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→72.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 10.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.339 / % reflection Rfree: 8 % / Rfactor Rwork: 0.306 |