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Yorodumi- PDB-3uqb: Crystal structure of a SMT Fusion PEPTIDYL-PROLYL CIS-TRANS ISOME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uqb | ||||||
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Title | Crystal structure of a SMT Fusion PEPTIDYL-PROLYL CIS-TRANS ISOMERASE with surface mutation D44G from Burkholderia pseudomallei complexed with FK506 | ||||||
Components | Ubiquitin-like protein SMT3, Peptidyl-prolyl cis-trans isomerase | ||||||
Keywords | Isomerase / protein binding / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / peptidylprolyl isomerase / condensed nuclear chromosome / peptidyl-prolyl cis-trans isomerase activity / protein tag activity / protein folding / identical protein binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2014 Title: A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins. Authors: Begley, D.W. / Fox, D. / Jenner, D. / Juli, C. / Pierce, P.G. / Abendroth, J. / Muruthi, M. / Safford, K. / Anderson, V. / Atkins, K. / Barnes, S.R. / Moen, S.O. / Raymond, A.C. / Stacy, R. ...Authors: Begley, D.W. / Fox, D. / Jenner, D. / Juli, C. / Pierce, P.G. / Abendroth, J. / Muruthi, M. / Safford, K. / Anderson, V. / Atkins, K. / Barnes, S.R. / Moen, S.O. / Raymond, A.C. / Stacy, R. / Myler, P.J. / Staker, B.L. / Harmer, N.J. / Norville, I.H. / Holzgrabe, U. / Sarkar-Tyson, M. / Edwards, T.E. / Lorimer, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uqb.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uqb.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 3uqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/3uqb ftp://data.pdbj.org/pub/pdb/validation_reports/uq/3uqb | HTTPS FTP |
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-Related structure data
Related structure data | 3uf8SC 3uqaC 3vawC 4dz2C 4dz3C 4fn2C 4g50C 4ggqC 4givC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22943.793 Da / Num. of mol.: 1 / Fragment: Q12306 residues 13-98, Q3JK38 residues 2-113 / Mutation: D44G Source method: isolated from a genetically manipulated source Details: Fusion Protein Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Burkholderia pseudomallei (bacteria) Strain: 1710b, S288c / Gene: BURPS1710b_A0907, SMT3, YDR510W, D9719.15 / Plasmid: pET28-HisSMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q12306, UniProt: Q3JK38, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-FK5 / |
#3: 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: 1.99 Å3/Da / Density % sol: 38.25 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9 Details: Internal tracking number 226421. PACT well B6. 0.1M MIB Buffer pH 9.0, 25.0% w/v PEG1500, 30% PEG400 Cryo. BUPSA.00130.A.D214 PD00190/6 23.7mg/ml, vapor diffusion, sitting drop, temperature ...Details: Internal tracking number 226421. PACT well B6. 0.1M MIB Buffer pH 9.0, 25.0% w/v PEG1500, 30% PEG400 Cryo. BUPSA.00130.A.D214 PD00190/6 23.7mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→38.5 Å / Num. all: 14561 / Num. obs: 14527 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.02 % / Biso Wilson estimate: 24.794 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.55 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB entry 3UF8 Resolution: 1.9→19.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.59 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.159 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.783 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 22.6918 Å / Origin y: 0.6483 Å / Origin z: 58.096 Å
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