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Yorodumi- PDB-1rqh: Propionibacterium shermanii transcarboxylase 5S subunit bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rqh | |||||||||
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Title | Propionibacterium shermanii transcarboxylase 5S subunit bound to pyruvic acid | |||||||||
Components | transcarboxylase 5S subunit | |||||||||
Keywords | TRANSFERASE / TIM-barrel / carbamylated lysine / transcarboxylase / cobalt / pyruvic acid | |||||||||
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 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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Remark 999 | SEQUENCE RESIDUE 184 EXISTS IN TWO ALTERNATE CONFORMATIONS: KCX, CARBAMYLATED LYSINE, AND LYS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rqh.cif.gz | 120 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rqh.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 1rqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/1rqh ftp://data.pdbj.org/pub/pdb/validation_reports/rq/1rqh | HTTPS FTP |
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-Related structure data
Related structure data | 1rqbSC 1rqeC 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: 59652.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: RESIDUE 184 EXISTS IN TWO ALTERNATE CONFORMATIONS: KCX AND LYS 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: GenBank: 38304072, UniProt: Q70AC7*PLUS, methylmalonyl-CoA carboxytransferase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-PYR / |
#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: 2.31 Å3/Da / Density % sol: 46.73 % |
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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 22, 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→30 Å / Num. all: 37671 / Num. obs: 34906 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 4.3 / % possible all: 80.5 |
-Processing
Software |
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Refinement | Method to determine structure: Isomorphous replacement Starting model: PDB ENTRY 1RQB Resolution: 2→28.09 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 370661.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESIDUE 184 EXISTS IN TWO ALTERNATE CONFORMATIONS: KCX AND LYS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.0483 Å2 / ksol: 0.32071 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→28.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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