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Yorodumi- PDB-2v8v: Crystal structure of mutant R322A of beta-alanine synthase from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v8v | ||||||
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Title | Crystal structure of mutant R322A of beta-alanine synthase from Saccharomyces kluyveri | ||||||
Components | BETA-ALANINE SYNTHASEBeta-ureidopropionase | ||||||
Keywords | HYDROLASE / DI-ZINC CENTER / AMIDOHYDROLASE / ALPHA AND BETA PROTEIN | ||||||
Function / homology | Function and homology information beta-ureidopropionase activity / beta-ureidopropionase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding Similarity search - Function | ||||||
Biological species | SACCHAROMYCES KLUYVERI (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Lundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structures of Yeast -Alanine Synthase Complexes Reveal the Mode of Substrate Binding and Large Scale Domain Closure Movements. Authors: Lundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Yeast Beta-Alanine Synthase Shares a Structural Scaffold and Origin with Dizinc-Dependent Exopeptidases Authors: Lundgren, S. / Gojkovic, Z. / Piskur, J. / Dobritzsch, D. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and Preliminary X-Ray Analysis of Beta-Alanine Synthase from the Yeast Saccharomyces Kluyveri Authors: Dobritzsch, D. / Gojkovic, Z. / Andersen, B. / Piskur, J. | ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v8v.cif.gz | 330.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v8v.ent.gz | 266.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/2v8v ftp://data.pdbj.org/pub/pdb/validation_reports/v8/2v8v | HTTPS FTP |
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-Related structure data
Related structure data | 2v8dC 2v8gC 2v8hC 1r43S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 51920.691 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-455 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES KLUYVERI (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q96W94, beta-ureidopropionase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-DTT / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ARG 322 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 322 TO ALA ...ENGINEERED | Nonpolymer details | 1,4-DITHIOTHRE | Sequence details | THE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION, THE LAST 20 ...THE N-TERMINAL METHIONINE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: TRISODIUM CITRATE PH 6.0, DIOXANE,ACETONE, DTT, NA-HEPES PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.874 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.874 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→45 Å / Num. obs: 44094 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.2 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R43 Resolution: 2.9→45 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.871 / SU B: 27.409 / SU ML: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→45 Å
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Refine LS restraints |
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