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Open data
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Basic information
Entry | Database: PDB / ID: 8hm4 | ||||||
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Title | Crystal structure of PPIase | ||||||
![]() | Peptidylprolyl isomerase | ||||||
![]() | ISOMERASE / CHAPERONE | ||||||
Function / homology | Trigger factor/SurA domain superfamily / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Peptidyl-prolyl cis-trans isomerase domain superfamily / peptidyl-prolyl cis-trans isomerase activity / PpiC domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, J.H. / Chen, Z. / Gao, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome. Authors: Jiang, K. / Li, W. / Tong, M. / Xu, J. / Chen, Z. / Yang, Y. / Zang, Y. / Jiao, X. / Liu, C. / Lim, B. / Jiang, X. / Wang, J. / Wu, D. / Wang, M. / Liu, S.J. / Shao, F. / Gao, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.8 KB | Display | ![]() |
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PDB format | ![]() | 141.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.6 KB | Display | ![]() |
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Full document | ![]() | 464.7 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 44.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hm1C ![]() 8hm2C ![]() 8hm3C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.998560204313, 0.0368004218624, -0.0390288010818), (0.00127226197204, -0.711120178755, -0.703069322839), (-0.0536274156808, -0.702106701519, 0.710049491211)Vector: 46. ...NCS oper: (Code: given Matrix: (-0.998560204313, 0.0368004218624, -0.0390288010818), Vector: |
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Components
#1: Protein | Mass: 49268.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M sodium citrate, 0.1M sodium chloride, 0.2M ammonium sulfate, 20% PEG2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): L / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3.79→37.44 Å / Num. obs: 13967 / % possible obs: 99.32 % / Redundancy: 6.6 % / Biso Wilson estimate: 159.1 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.038 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 3.79→3.93 Å / Num. unique obs: 1342 / CC1/2: 0.608 / Rpim(I) all: 0.397 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 206.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.79→37.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 5.45990744546 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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