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- PDB-6zag: Room temperature XFEL Isopenicillin N synthase structure in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zag | ||||||||||||||||||||||||||||||||||||||||||
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Title | Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and ACV after exposure to dioxygen for 500ms. | ||||||||||||||||||||||||||||||||||||||||||
![]() | Isopenicillin N synthase | ||||||||||||||||||||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / Isopenicillin N synthase / oxygen binding / XFEL / time-resolved crystallography | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
![]() | Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K. / Pharm, C. / McDonough, M.A. / Leissing, T.M. / Aller, P. / Butryn, A. / Linyard, J. / Lang, P. ...Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K. / Pharm, C. / McDonough, M.A. / Leissing, T.M. / Aller, P. / Butryn, A. / Linyard, J. / Lang, P. / Brem, J. / Fuller, F.D. / Batyuk, A. / Hunter, M.S. / Pettinati, I. / Clifton, I.J. / Alonso-Mori, R. / Gul, S. / Young, I. / Kim, I. / Bhowmick, A. / ORiordan, L. / Brewster, A.S. / Claridge, T.D.W. / Sauter, N.K. / Yachandra, V. / Yano, J. / Kern, J.F. / Orville, A.M. / Schofield, C.J. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis. Authors: Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K.D. / Linyard, J.D.S. / Aller, P. / Pham, C.C. / Makita, H. / Clifton, I. / McDonough, M.A. / Leissing, T.M. / Shutin, D. / Lang, P.A. / Butryn, A. / ...Authors: Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K.D. / Linyard, J.D.S. / Aller, P. / Pham, C.C. / Makita, H. / Clifton, I. / McDonough, M.A. / Leissing, T.M. / Shutin, D. / Lang, P.A. / Butryn, A. / Brem, J. / Gul, S. / Fuller, F.D. / Kim, I.S. / Cheah, M.H. / Fransson, T. / Bhowmick, A. / Young, I.D. / O'Riordan, L. / Brewster, A.S. / Pettinati, I. / Doyle, M. / Joti, Y. / Owada, S. / Tono, K. / Batyuk, A. / Hunter, M.S. / Alonso-Mori, R. / Bergmann, U. / Owen, R.L. / Sauter, N.K. / Claridge, T.D.W. / Robinson, C.V. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Orville, A.M. / Schofield, C.J. | ||||||||||||||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 251.2 KB | Display | ![]() |
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PDB format | ![]() | 167.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 359.9 KB | Display | ![]() |
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Full document | ![]() | 359.9 KB | Display | |
Data in XML | ![]() | 15.4 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y0pC ![]() 6zaeC ![]() 6zafC ![]() 6zahC ![]() 6zaiC ![]() 6zajC ![]() 6zalC ![]() 6zamC ![]() 6zanC ![]() 6zaoC ![]() 6zapC ![]() 6zaqC ![]() 6zw8C ![]() 1blzS 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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Components
#1: Protein | Mass: 37563.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ipnA, ips, AN2622 / Plasmid: plasmid / Production host: ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-ACV / | #4: Chemical | ChemComp-FE2 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.95 % / Description: needles - size range 40-60um x 3 um x 3 um |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 8.5 / Details: 1.7 M Li2SO4, 0.1 M TRIS pH 8.5 |
-Data collection
Diffraction | Mean temperature: 298 K / Ambient temp details: room temperature / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Dec 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.30166 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20.29 Å / Num. obs: 64897 / % possible obs: 99.95 % / Redundancy: 103.55 % / Biso Wilson estimate: 19.4464311825 Å2 / CC1/2: 0.98 / R split: 0.148 / Net I/σ(I): 35.087 |
Reflection shell | Resolution: 1.4→1.424 Å / Redundancy: 17.73 % / Mean I/σ(I) obs: 0.404 / Num. unique obs: 3173 / CC1/2: 0.023 / R split: 1.311 / % possible all: 99.97 |
Serial crystallography sample delivery | Method: injection |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1BLZ Resolution: 1.4001→20.2867 Å / SU ML: 0.1991 / Cross valid method: THROUGHOUT / σ(F): 1.3276 / Phase error: 23.1218 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: 29.5166 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4001→20.2867 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -10.6719894612 Å / Origin y: 0.200336158562 Å / Origin z: -2.69767892267 Å
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Refinement TLS group | Selection details: all |