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- PDB-7z3d: XFEL structure of Class Ib ribonucleotide reductase dimanganese(I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z3d | ||||||||||||||||||
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Title | XFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with oxidized NrdI from Bacillus cereus | ||||||||||||||||||
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![]() | OXIDOREDUCTASE / Ribonucleotide reductase R2b / Class Ib RNR / Flavoprotein / Metalloenzyme / ferritin-like superfamily / dimanganese cofactor / XFEL | ||||||||||||||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein modification process / FMN binding / membrane / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | John, J. / Lebrette, H. / Aurelius, O. / Hogbom, M. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography. Authors: John, J. / Aurelius, O. / Srinivas, V. / Saura, P. / Kim, I.S. / Bhowmick, A. / Simon, P.S. / Dasgupta, M. / Pham, C. / Gul, S. / Sutherlin, K.D. / Aller, P. / Butryn, A. / Orville, A.M. / ...Authors: John, J. / Aurelius, O. / Srinivas, V. / Saura, P. / Kim, I.S. / Bhowmick, A. / Simon, P.S. / Dasgupta, M. / Pham, C. / Gul, S. / Sutherlin, K.D. / Aller, P. / Butryn, A. / Orville, A.M. / Cheah, M.H. / Owada, S. / Tono, K. / Fuller, F.D. / Batyuk, A. / Brewster, A.S. / Sauter, N.K. / Yachandra, V.K. / Yano, J. / Kaila, V.R.I. / Kern, J. / Lebrette, H. / Hogbom, M. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.3 KB | Display | ![]() |
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PDB format | ![]() | 153 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z3eC ![]() 4bmoS S: Starting model for refinement 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37052.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711 Gene: BC_1355 / Production host: ![]() ![]() References: UniProt: Q81G55, ribonucleoside-diphosphate reductase |
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#2: Protein | Mass: 13539.261 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nrdI, A9485_05295, B4082_4779, BKK64_22520, BLD50_28200, BLX06_07420, C1N66_03050, C6A78_17740, C6Y54_16250, CJ306_07140, CN357_26430, CN553_06005, CN980_12615, COD77_14575, COI69_30475, COI98_ ...Gene: nrdI, A9485_05295, B4082_4779, BKK64_22520, BLD50_28200, BLX06_07420, C1N66_03050, C6A78_17740, C6Y54_16250, CJ306_07140, CN357_26430, CN553_06005, CN980_12615, COD77_14575, COI69_30475, COI98_10480, COM79_20950, CON36_20815, CON37_10850, CSW12_06330, D0437_06525, DR116_0000380, DX932_00180, E2F98_13910, F8165_13725, F8172_22390, FC692_08670, FC695_16850, FC702_30940, FORC47_1246, GE376_06770, JDS76_16260, TU58_02775, WR52_06765 Production host: ![]() ![]() |
-Non-polymers , 4 types, 163 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-UNX / | #5: Chemical | ChemComp-FMN / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % / Description: Yellow rhombohedron shaped crystals |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 5 / Details: 0.1 M MnCl2, 0.1 M sodium acetate 5.0, 5% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Dec 9, 2018 / Frequency: 30 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.300734 Å / Relative weight: 1 |
Reflection | Resolution: 2→51.59 Å / Num. obs: 38319 / % possible obs: 99.91 % / Redundancy: 66.94 % / Biso Wilson estimate: 35.45 Å2 / CC1/2: 0.989 / R split: 0.111 / Net I/σ(I): 3.247 |
Reflection shell | Resolution: 2→2.034 Å / Redundancy: 25.42 % / Mean I/σ(I) obs: 0.654 / Num. unique obs: 1881 / CC1/2: 0.32 / R split: 0.863 / % possible all: 100 |
Serial crystallography measurement | Collection time total: 0.5 hours / Collimation: compound refractive lenses / Pulse duration: 35 fsec. / Pulse energy: 4 µJ / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 30 Hz |
Serial crystallography sample delivery | Description: drop on tape combined with acoustic droplet ejection Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: mother liquor / Description: acoustic droplet injection / Flow rate: 8 µL/min / Injector temperature: 298 K / Power by: focused acoustic pulse |
Serial crystallography data reduction | Lattices indexed: 14357 / XFEL run numbers: 56-61 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4bmo Resolution: 2→24.17 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.48 / Stereochemistry target values: ML
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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 max: 120.31 Å2 / Biso mean: 47.4506 Å2 / Biso min: 21.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→24.17 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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