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- PDB-4bmz: Structure of futalosine hydrolase mutant of Helicobacter pylori s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bmz | ||||||
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Title | Structure of futalosine hydrolase mutant of Helicobacter pylori strain 26695 | ||||||
![]() | MTA/SAH NUCLEOSIDASE | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, R.Q. / Offen, W.A. / Stubbs, K.A. / Davies, G.J. | ||||||
![]() | ![]() Title: Structural Enzymology of Helicobacter Pylori Methylthioadenosine Nucleosidase in the Futalosine Pathway Authors: Kim, R.Q. / Offen, W.A. / Davies, G.J. / Stubbs, K.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.4 KB | Display | ![]() |
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PDB format | ![]() | 148 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bmxSC ![]() 4bmyC ![]() 4bn0C 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: 27406.426 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O24915, adenosylhomocysteine nucleosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.2 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS-TRIS PH 5.5, 25% PEG-3350, 0.2 M MGCL2.6H2O |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9163 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→55.48 Å / Num. obs: 40405 / % possible obs: 98.4 % / Observed criterion σ(I): 6 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.79→1.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BMX Resolution: 1.79→55.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.211 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.123 / 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 / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→55.55 Å
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Refine LS restraints |
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