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Yorodumi- PDB-6s62: Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s62 | |||||||||
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Title | Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in apo form. | |||||||||
Components | Propionate catabolic protein PrpD | |||||||||
Keywords | ISOMERASE / 2-methlycitrate dehydratase / MmgE/PrpD / propionate metabolism | |||||||||
Function / homology | Function and homology information 2-methylcitrate dehydratase / 2-methylcitrate dehydratase activity / propionate metabolic process, methylcitrate cycle / 2 iron, 2 sulfur cluster binding Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | |||||||||
Authors | Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Crystal structure of 2-methylcitrate dehydratase (PrpD) from Pseudomonas aeruginosa in apo form. Authors: Wijaya, A.J. / Brear, P. / Dolan, S.K. / Welch, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s62.cif.gz | 548.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s62.ent.gz | 454.9 KB | Display | PDB format |
PDBx/mmJSON format | 6s62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s62_validation.pdf.gz | 469 KB | Display | wwPDB validaton report |
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Full document | 6s62_full_validation.pdf.gz | 499.2 KB | Display | |
Data in XML | 6s62_validation.xml.gz | 93.1 KB | Display | |
Data in CIF | 6s62_validation.cif.gz | 129.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/6s62 ftp://data.pdbj.org/pub/pdb/validation_reports/s6/6s62 | HTTPS FTP |
-Related structure data
Related structure data | 1szqS S: Starting model for refinement |
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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: 54953.602 Da / Num. of mol.: 6 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) Gene: prpD, PA0792 Variant: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I5E6 #2: 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: 2.64 Å3/Da / Density % sol: 53.4 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS.HCl pH 8.5, 15-25 %(w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.36→113.25 Å / Num. obs: 140797 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.72 Å2 / CC1/2: 0.958 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.074 / Rrim(I) all: 0.146 / Net I/σ(I): 7.2 / Num. measured all: 518784 / Scaling rejects: 590 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.4 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SZQ Resolution: 2.36→113.175 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 201.18 Å2 / Biso mean: 34.2104 Å2 / Biso min: 9.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.36→113.175 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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