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Open data
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Basic information
Entry | Database: PDB / ID: 5ov4 | ||||||
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Title | Bacillus megaterium porphobilinogen deaminase D82A mutant | ||||||
![]() | Porphobilinogen deaminase | ||||||
![]() | TRANSFERASE / Deaminase / mutation / domain movements / cofactor | ||||||
Function / homology | ![]() hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / heme biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, J. / Erskine, P. / Coker, A.R. / Wood, S.P. / Cooper, J.B. | ||||||
![]() | ![]() Title: Structural studies of domain movement in active-site mutants of porphobilinogen deaminase from Bacillus megaterium. Authors: Guo, J. / Erskine, P. / Coker, A.R. / Wood, S.P. / Cooper, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.1 KB | Display | ![]() |
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PDB format | ![]() | 50.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428 KB | Display | ![]() |
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Full document | ![]() | 431.2 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ov5C ![]() 5ov6C ![]() 4mlvS S: Starting model for refinement C: citing same article ( |
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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: 34381.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.86 % Description: Clusters formed by thin plates with a dark yellow colour |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.7 Details: 0.2 M ammonium acetate, 0.1 M sodium acetate pH 3.7, 25 % PEG 4000 PH range: 3.5-4.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→29.564 Å / Num. obs: 8221 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 51.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.151 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.69→2.76 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 579 / CC1/2: 0.797 / Rrim(I) all: 0.585 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MLV Resolution: 2.692→29.564 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 22.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.692→29.564 Å
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Refine LS restraints |
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LS refinement shell |
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