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Yorodumi- PDB-2xz0: The Structure of the 2:1 (Partially Occupied) Complex Between Ste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xz0 | ||||||
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Title | The Structure of the 2:1 (Partially Occupied) Complex Between Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean) and Acyl Carrier Protein. | ||||||
Components |
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Keywords | OXIDOREDUCTASE/LIPID BINDING PROTEIN / OXIDOREDUCTASE-LIPID BINDING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information stearoyl-[acyl-carrier-protein] 9-desaturase / : / stearoyl-[ACP] desaturase activity / phosphopantetheine binding / acyl carrier activity / chloroplast / fatty acid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | RICINUS COMMUNIS (castor bean) SPINACIA OLERACEA (spinach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Moche, M. / Guy, J.E. / Whittle, E. / Lengqvist, J. / Shanklin, J. / Lindqvist, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Remote Control of Regioselectivity in Acyl-Acyl Carrier Protein-Desaturases. Authors: Guy, J.E. / Whittle, E. / Moche, M. / Lengqvist, J. / 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 | 2xz0.cif.gz | 472.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xz0.ent.gz | 392.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xz0_validation.pdf.gz | 475.6 KB | Display | wwPDB validaton report |
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Full document | 2xz0_full_validation.pdf.gz | 495.6 KB | Display | |
Data in XML | 2xz0_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 2xz0_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/2xz0 ftp://data.pdbj.org/pub/pdb/validation_reports/xz/2xz0 | HTTPS FTP |
-Related structure data
Related structure data | 2xz1C 1afrS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 18 - 363 / Label seq-ID: 18 - 363
NCS oper:
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 41703.312 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RICINUS COMMUNIS (castor bean) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P22337, stearoyl-[acyl-carrier-protein] 9-desaturase #2: Protein | | Mass: 8924.858 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SER38 (SEP IN SEQUENCE) IS A PHOSPHOSERINE / Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07854 |
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-Non-polymers , 4 types, 33 molecules
#3: Chemical | ChemComp-FE / #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | SEQUENCE AS DESCRIBED IN BROADWATER |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.37 % / Description: NONE |
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Crystal grow | pH: 5.62 Details: 4-5% PEG 20000, 8% PEG 550MME, 180MM SODIUM BROMIDE, 100MM SODIUM ACETATE PH 5.62, 15% GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 33376 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AFR Resolution: 3→29.28 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.887 / SU B: 46.969 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 98.175 Å2
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Refinement step | Cycle: LAST / Resolution: 3→29.28 Å
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Refine LS restraints |
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