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Yorodumi- PDB-2xz1: The Structure of the 2:2 (Fully Occupied) Complex Between Stearoy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xz1 | ||||||
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Title | The Structure of the 2:2 (Fully 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: 3.35 Å | ||||||
Authors | Guy, J.E. / Moche, M. / 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 | 2xz1.cif.gz | 358.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xz1.ent.gz | 296.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xz1_validation.pdf.gz | 739.1 KB | Display | wwPDB validaton report |
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Full document | 2xz1_full_validation.pdf.gz | 748 KB | Display | |
Data in XML | 2xz1_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 2xz1_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/2xz1 ftp://data.pdbj.org/pub/pdb/validation_reports/xz/2xz1 | HTTPS FTP |
-Related structure data
Related structure data | 2xz0C 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:
NCS ensembles :
NCS oper:
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 41703.312 Da / Num. of mol.: 2 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.: 2 Source method: isolated from a genetically manipulated source Details: SER38 CHAIN D IS A PHOSPHOSERINE, IN CHAIN C IT IS ALSO LINKED TO A FRAGMENT OF PANTETHEINE Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07854 |
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-Non-polymers , 4 types, 9 molecules
#3: Chemical | ChemComp-FE / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PNY / ( | |
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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: 2.91 Å3/Da / Density % sol: 57.69 % / Description: NONE |
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Crystal grow | pH: 5.8 Details: 16-20% MPD,6-8% PEG20000, 0.1M SODIUM CACODYLATE PH 5.8, 4-6% ACETONITRILE |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→20 Å / Num. obs: 16101 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.35→3.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AFR Resolution: 3.35→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 60.836 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.585 / 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: 107.329 Å2
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Refinement step | Cycle: LAST / Resolution: 3.35→20 Å
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Refine LS restraints |
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