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Yorodumi- PDB-5xum: Crystal structure of Thermotoga maritima holo-[acyl-carrier-prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xum | ||||||
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Title | Crystal structure of Thermotoga maritima holo-[acyl-carrier-protein] synthase (AcpS) | ||||||
Components | Holo-[acyl-carrier-protein] synthase | ||||||
Keywords | TRANSFERASE / Gram-negative bacteria / phosphopantetheinyl transferase / homotrimer | ||||||
Function / homology | Function and homology information holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Liao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S. | ||||||
Citation | Journal: To Be Published Title: Crystal structures of acyl carrier protein synthases (AcpS) from three Gram-negative bacteria Authors: Liao, Y.P. / Wang, D.L. / Yin, D.P. / Zhang, Q.Y. / Wang, Y.M. / Wang, D.Q. / Zhu, H.X. / Chen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xum.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xum.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 5xum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xum_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 5xum_full_validation.pdf.gz | 431.5 KB | Display | |
Data in XML | 5xum_validation.xml.gz | 9 KB | Display | |
Data in CIF | 5xum_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/5xum ftp://data.pdbj.org/pub/pdb/validation_reports/xu/5xum | HTTPS FTP |
-Related structure data
Related structure data | 5xu7C 5xuhC 5xukC 1f80S 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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Unit cell |
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-Components
#1: Protein | Mass: 19322.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: acpS, TM_0692 / Production host: Escherichia coli (E. coli) References: UniProt: Q9WZF6, holo-[acyl-carrier-protein] synthase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.27 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 8 / Details: 10mM Tris-HCl pH 8.0, 100mM NaCl, 10mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2014 |
Radiation | Monochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→63.185 Å / Num. obs: 14645 / % possible obs: 98.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 37.39 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.038 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2146 / Rpim(I) all: 0.272 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F80 Resolution: 2.1→63.18 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.112 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.678 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→63.18 Å
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Refine LS restraints |
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