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- PDB-2ybo: The x-ray structure of the SAM-dependent uroporphyrinogen III met... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ybo | ||||||
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Title | The x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH | ||||||
![]() | METHYLTRANSFERASE | ||||||
![]() | TRANSFERASE / SUMT / NIRE / HEME D1 BIOSYNTHESIS | ||||||
Function / homology | ![]() uroporphyrinogen-III C-methyltransferase / uroporphyrin-III C-methyltransferase activity / siroheme biosynthetic process / cobalamin biosynthetic process / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Storbeck, S. / Saha, S. / Krausze, J. / Klink, B.U. / Heinz, D.W. / Layer, G. | ||||||
![]() | ![]() Title: Crystal Structure of the Heme D1 Biosynthesis Enzyme Nire in Complex with its Substrate Reveals New Insights Into the Catalytic Mechanism of S-Adenosyl-L-Methionine-Dependent Uroporphyrinogen ...Title: Crystal Structure of the Heme D1 Biosynthesis Enzyme Nire in Complex with its Substrate Reveals New Insights Into the Catalytic Mechanism of S-Adenosyl-L-Methionine-Dependent Uroporphyrinogen III Methyltransferases. Authors: Storbeck, S. / Saha, S. / Krausze, J. / Klink, B.U. / Heinz, D.W. / Layer, 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 | ![]() | 111.8 KB | Display | ![]() |
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PDB format | ![]() | 85.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 810.4 KB | Display | ![]() |
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Full document | ![]() | 813 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ybqC ![]() 1s4dS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31402.012 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-279 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P95417, uroporphyrinogen-III C-methyltransferase |
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#2: Chemical | ChemComp-SAH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE |
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Crystal grow | pH: 8 Details: PROTEIN WAS CRYSTALLIZED FROM 24% PEG 6000, 0.1 M TRIS PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Oct 22, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.31 Å / Num. obs: 19360 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.19 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.58 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1S4D Resolution: 2→26.915 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.853 / SU B: 12.098 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.231 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.459 Å2
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Refinement step | Cycle: LAST / Resolution: 2→26.915 Å
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Refine LS restraints |
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