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Open data
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Basic information
Entry | Database: PDB / ID: 1s3h | ||||||
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Title | Propionibacterium shermanii transcarboxylase 5S subunit A59T | ||||||
![]() | transcarboxylase 5S subunit | ||||||
![]() | TRANSFERASE / TIM-barrel / carbamylated lysine / transcarboxylase / cobalt | ||||||
Function / homology | ![]() methylmalonyl-CoA carboxytransferase / methylmalonyl-CoA carboxytransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Hall, P.R. / Zheng, R. / Antony, L. / Pusztai-Carey, M. / Carey, P.R. / Yee, V.C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.6 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 444.7 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rqbSC ![]() 1rqeC ![]() 1rqhC ![]() 1rr2C ![]() 1u5jC ![]() 1s27 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The asymmetric unit contains a monomer. The biological dimer is formed by the following transformation: -1.0000*x+ 0.0000*y+ 0.0000*z+ 192.516 0.0000*x+ 1.0000*y+ 0.0000*z+ 0.000 0.0000*x+ 0.0000*y+ -1.0000*z+ 39.359 |
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Components
#1: Protein | Mass: 59682.496 Da / Num. of mol.: 1 / Mutation: A59T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / Gene: 5S / Plasmid: pETBlue-2 / Production host: ![]() ![]() References: UniProt: Q70AC7, methylmalonyl-CoA carboxytransferase |
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#2: Chemical | ChemComp-CO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.03 % |
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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: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 23, 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: 19598 / Num. obs: 18621 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 6.9 / % possible all: 87.5 |
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Processing
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Refinement | Method to determine structure: Isomorphous replacement Starting model: PDB ENTRY 1RQB Resolution: 2.5→29.19 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 226821.14 / 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: 10 Å2 / ksol: 0.300775 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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