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Yorodumi- PDB-1rqe: Propionibacterium shermanii transcarboxylase 5S subunit bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rqe | ||||||
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Title | Propionibacterium shermanii transcarboxylase 5S subunit bound to oxaloacetate | ||||||
Components | transcarboxylase 5S subunit | ||||||
Keywords | TRANSFERASE / TIM-barrel / carbamylated lysine / transcarboxylase / cobalt / oxaloacetate | ||||||
Function / homology | Function and homology information methylmalonyl-CoA carboxytransferase / methylmalonyl-CoA carboxytransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Propionibacterium freudenreichii subsp. shermanii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Isomorphous replacement / Resolution: 2.5 Å | ||||||
Authors | Hall, P.R. / Zheng, R. / Antony, L. / Pusztai-Carey, M. / Carey, P.R. / Yee, V.C. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit. Authors: Hall, P.R. / Zheng, R. / Antony, L. / Pusztai-Carey, M. / Carey, P.R. / Yee, V.C. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Expression and crystallization of several forms of the Propionibacterium shermanii transcarboxylase 5S subunit Authors: Hall, P.R. / Zheng, R. / Pusztai-Carey, M. / van den Akker, F. / Carey, P.R. / Yee, V.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rqe.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rqe.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 1rqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/1rqe ftp://data.pdbj.org/pub/pdb/validation_reports/rq/1rqe | HTTPS FTP |
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-Related structure data
Related structure data | 1rqbSC 1rqhC 1rr2C 1s3hC 1u5jC 1s27 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 59609.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria) Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / Gene: 5S / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLacI References: UniProt: Q70AC7, methylmalonyl-CoA carboxytransferase |
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#2: Chemical | ChemComp-OAA / |
#3: Chemical | ChemComp-CO / |
#4: 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: 2.29 Å3/Da / Density % sol: 46.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 4000, Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 3, 2003 |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 19290 / Num. obs: 16792 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 7.2 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: Isomorphous replacement Starting model: PDB ENTRY 1RQB Resolution: 2.5→27.17 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 281546.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.3617 Å2 / ksol: 0.305673 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→27.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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