+Open data
-Basic information
Entry | Database: PDB / ID: 2uw1 | ||||||
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Title | Ivy Desaturase Structure | ||||||
Components | (PLASTID DELTA4 MULTIFUNCTIONAL ACYL-ACYL CARRIER PROTEIN ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSFER / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS | ||||||
Function / homology | Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Orthogonal Bundle / Mainly Alpha / : / (3R)-3-HYDROXY-5,5-DIMETHYLHEXANOIC ACID Function and homology information | ||||||
Biological species | HEDERA HELIX (English ivy) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Guy, J.E. / Whittle, E. / Kumaran, D. / Lindqvist, Y. / Shanklin, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: The Crystal Structure of the Ivy {Delta}4-16:0-Acp Desaturase Reveals Structural Details of the Oxidized Active Site and Potential Determinants of Regioselectivity. Authors: Guy, J.E. / Whittle, E. / Kumaran, D. / Lindqvist, Y. / Shanklin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uw1.cif.gz | 162.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uw1.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 2uw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uw1_validation.pdf.gz | 450.1 KB | Display | wwPDB validaton report |
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Full document | 2uw1_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 2uw1_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 2uw1_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/2uw1 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/2uw1 | HTTPS FTP |
-Related structure data
Related structure data | 1afrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.17958, 0.98338, 0.02669), Vector: |
-Components
-PLASTID DELTA4 MULTIFUNCTIONAL ACYL-ACYL CARRIER PROTEIN ... , 2 types, 2 molecules AB
#1: Protein | Mass: 38986.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HEDERA HELIX (English ivy) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: EC: 1.14.99.6 |
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#2: Protein | Mass: 38980.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HEDERA HELIX (English ivy) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: EC: 1.14.99.6 |
-Non-polymers , 4 types, 551 molecules
#3: Chemical | ChemComp-FE / #4: Chemical | #5: Chemical | #6: 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: 2.24 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | pH: 7 / Details: pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 56078 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.96 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AFR Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.338 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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