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Yorodumi- PDB-3vz2: Structural insights into substrate and cofactor selection by sp2771 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vz2 | ||||||
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Title | Structural insights into substrate and cofactor selection by sp2771 | ||||||
Components | Succinate-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / substrate selection / cofactor preference | ||||||
Function / homology | Function and homology information succinate-semialdehyde dehydrogenase (NAD+) activity / aldehyde dehydrogenase [NAD(P)+] activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Synechococcus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Yuan, Y.A. / Yuan, Z. / Yin, B. / Wei, D. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2013 Title: Structural basis for cofactor and substrate selection by cyanobacterium succinic semialdehyde dehydrogenase Authors: Yuan, Z. / Yin, B. / Wei, D. / Yuan, Y.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vz2.cif.gz | 340.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vz2.ent.gz | 278.8 KB | Display | PDB format |
PDBx/mmJSON format | 3vz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vz2_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 3vz2_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 3vz2_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 3vz2_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/3vz2 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/3vz2 | HTTPS FTP |
-Related structure data
Related structure data | 3vz0C 3vz1C 3vz3C 3jz4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50856.938 Da / Num. of mol.: 2 / Mutation: S419A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus (bacteria) / Strain: ATCC 27264 / PCC 7002 / PR-6 / Gene: SYNPCC7002_A2771 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XMM6 #2: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 5000 MME, Tascimate, HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 32970 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Rsym value: 0.072 |
Reflection shell | Resolution: 2.5→2.54 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3JZ4 Resolution: 2.5→42.12 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 17.509 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.585 / ESU R Free: 0.282 / 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: 27.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→42.12 Å
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Refine LS restraints |
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