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Yorodumi- PDB-5vj1: Crystal structure of a Pseudomonas malonate decarboxylase hetero-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vj1 | ||||||
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Title | Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with coenzyme A | ||||||
Components |
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Keywords | TRANSFERASE / acetyl-CoA carboxylase / coa transferase / acp transferase | ||||||
Function / homology | Function and homology information malonyl-S-ACP:biotin-protein carboxyltransferase / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / carboxy-lyase activity / acyl carrier activity / fatty acid biosynthetic process / transferase activity / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å | ||||||
Authors | Maderbocus, R. / Tong, L. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer. Authors: Maderbocus, R. / Fields, B.L. / Hamilton, K. / Luo, S. / Tran, T.H. / Dietrich, L.E.P. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vj1.cif.gz | 455.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vj1.ent.gz | 367.2 KB | Display | PDB format |
PDBx/mmJSON format | 5vj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vj1_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5vj1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5vj1_validation.xml.gz | 80.8 KB | Display | |
Data in CIF | 5vj1_validation.cif.gz | 110.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/5vj1 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/5vj1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 4 types, 8 molecules AICKDLEM
#1: Protein | Mass: 61501.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: mdcA, PA0208 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6T0 #2: Protein | Mass: 10692.981 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria) Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: mdcC, PFL_5818 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K4F7 #3: Protein | Mass: 30371.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: madC, mdcD, AO964_31600, AOY09_06294, BH593_13640, PAERUG_E15_London_28_01_14_07061, PAERUG_P32_London_17_VIM_2_10_11_04127, PAMH19_0209 Production host: Escherichia coli (E. coli) References: UniProt: A0A071KS24, UniProt: Q9I6S7*PLUS, malonyl-S-ACP:biotin-protein carboxyltransferase, methylmalonyl-CoA carboxytransferase #4: Protein | Mass: 30351.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: madD, AO964_31595, AOY09_06293, PAERUG_E15_London_28_01_14_07062, PAERUG_P32_London_17_VIM_2_10_11_04128 Production host: Escherichia coli (E. coli) References: UniProt: A0A0C6EV56, UniProt: Q9I6S6*PLUS, malonyl-S-ACP:biotin-protein carboxyltransferase |
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-Non-polymers , 2 types, 3 molecules
#5: Chemical | ChemComp-CL / |
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#6: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG3350 and 8% Tacsimate / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2016 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 63210 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 1.7 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.995→47.901 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.995→47.901 Å
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Refine LS restraints |
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LS refinement shell |
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