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Open data
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Basic information
Entry | Database: PDB / ID: 1abs | ||||||
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Title | PHOTOLYSED CARBONMONOXY-MYOGLOBIN AT 20 K | ||||||
![]() | MYOGLOBIN | ||||||
![]() | OXYGEN STORAGE / INTERMEDIATE IN LIGAND BINDING / RESPIRATORY PROTEIN | ||||||
Function / homology | ![]() nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schlichting, I. / Berendzen, J. / Phillips Jr., G.N. / Sweet, R.M. | ||||||
![]() | ![]() Title: Crystal structure of photolysed carbonmonoxy-myoglobin. Authors: Schlichting, I. / Berendzen, J. / Phillips Jr., G.N. / Sweet, R.M. #1: ![]() Title: Crystal Structure of Myoglobin from a Synthetic Gene Authors: Phillips Jr., G.N. / Arduini, R.M. / Springer, B.A. / Sligar, S.G. #2: ![]() Title: High-Level Expression of Sperm Whale Myoglobin in Escherichia Coli Authors: Springer, B.A. / Sligar, S.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.8 KB | Display | ![]() |
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PDB format | ![]() | 33.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 821.4 KB | Display | ![]() |
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Full document | ![]() | 825.5 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2mgkS 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: 17365.164 Da / Num. of mol.: 1 / Mutation: D122N Source method: isolated from a genetically manipulated source Details: HEME BOUND TO HIS-93, PHOTOLYSED CO ATOP HEME / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-CMO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.12 % Description: DATA WERE COLLECTED UNDER CONTINUOUS ILLUMINATION USING AN OPEN FLOW HELIUM CRYOSTAT FOR COOLING. | |||||||||||||||||||||||||
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Crystal grow | pH: 9 Details: PROTEIN WAS CRYSTALLIZED FROM 3.6 M AMMONIUM SULFATE. CRYSTALS WER SOAKED FOR 1 HOUR IN A THOROUGHLY DEGASSED AND N2 - SATURATED CRYOPROTECTANT SOLUTION MADE BY ADDITION OF 100 MG SUCROSE, ...Details: PROTEIN WAS CRYSTALLIZED FROM 3.6 M AMMONIUM SULFATE. CRYSTALS WER SOAKED FOR 1 HOUR IN A THOROUGHLY DEGASSED AND N2 - SATURATED CRYOPROTECTANT SOLUTION MADE BY ADDITION OF 100 MG SUCROSE, 100 MG GLUCOSE AND 8 MG NA-DITHIONATE TO 1 ML OF 70% SATURATED AMMONIUM SULFATE WITH 50 MM TRIS. HCL PH 9.0. THEN THE SOLUTION WAS EXCHANGED AGAINST A CO SATURATED ONE. DISTINCT COLOR CHANGES ACCOMPANIED THE FORMATION OF UNLIGATED MYOGLOBIN FROM MET-MB AND MBCO FROM UNLIGATED MB. | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 20 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Mar 1, 1994 / Details: YES |
Radiation | Monochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.5 Å / Num. obs: 30947 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.063 / Rsym value: 0.068 |
Reflection shell | Resolution: 1.5→1.7 Å / % possible all: 78 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 93946 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 78 % |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 2MGK Resolution: 1.5→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / σ(F): 0 Details: HEME PARAMETERS WERE RELAXED TO ALLOW FOR REFINEMENT OF UNLIGATED, PHOTOLYSED, AND CO-BOUND COMPLEX.
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Displacement parameters | Biso mean: 6.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→7 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: N.A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.57 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor all: 0.263 |