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- PDB-8gfd: Crystal structure of soluble lytic transglycosylase Cj0843 of Cam... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gfd | ||||||
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Title | Crystal structure of soluble lytic transglycosylase Cj0843 of Campylobacter jejuni in complex with Z3252 inhibitor | ||||||
![]() | Lytic transglycosylase domain-containing protein | ||||||
![]() | LYASE/LYASE INHIBITOR / soluble lytic transglycosylase / inhibitor / LYASE / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | ![]() lytic transglycosylase activity / peptidoglycan metabolic process / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van den Akker, F. / Kumar, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter jejuni via targeting different sites with different scaffolds. Authors: Kumar, V. / Boorman, J. / Greenlee, W.J. / Zeng, X. / Lin, J. / van den Akker, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.6 KB | Display | ![]() |
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PDB format | ![]() | 97.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8gezC ![]() 8gf0C ![]() 8gf1C ![]() 8gfbC ![]() 8gfcC ![]() 8gfeC ![]() 8gffC ![]() 8gfgC ![]() 8gfhC ![]() 8gfiC ![]() 8gfjC ![]() 8gflC ![]() 8gfmC ![]() 8gfpC ![]() 8gfqC ![]() 8gfsC ![]() 6cf9S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 63644.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: A0X18_03655, A0X31_01845, A9372_04065, APU74_07480, B1933_07625, BBS05_05650, BCB47_05730, BED64_07690, C3I22_05260, C3I27_06990, C3I35_05175, C7N26_08315, CJ274_08505, CV323_05370, CWD74_ ...Gene: A0X18_03655, A0X31_01845, A9372_04065, APU74_07480, B1933_07625, BBS05_05650, BCB47_05730, BED64_07690, C3I22_05260, C3I27_06990, C3I35_05175, C7N26_08315, CJ274_08505, CV323_05370, CWD74_05755, D0W34_08355, D4Q41_06000, D5I02_03510, D6H33_08420, DPG08_07275, DUX97_06720, DUY05_08000, DWS06_05135, DYE84_06365, E7R20_02805, EAX31_05720, EC071_05580, F0166_06250, F6982_06065, F7521_08930, F7J47_05300, F7U05_05765, F8803_06810, F9778_04965, FCR67_06545, FPD29_09025, FPT92_05795, FV831_05555, FV933_07400, FVI24_07230, FVM64_02425, FVM77_01160, FW220_07595, FW611_08035, FW976_03985, FWA25_07655, FY101_03890, FZ445_05005, FZ878_07970, FZW01_06295, G3M94_001083, GAX22_07420, GCI37_01695, GI172_07425, GIT96_06475, GJ442_07755, GK482_04850, GK486_00445, GL007_04270, GL031_07375, GM780_07860, GMG42_07100, GN862_07225, GNO13_05645, GNO32_03000, GPD80_07165, GRH33_07480, GRM82_06860, GRO30_05060, GRS20_08245, GSH24_05325, GTJ31_06080, GTV40_06285, GTV58_05620, GWW45_06140, GY415_000965, GZ489_001419, GZ499_001624, GZ502_000976, GZ518_001219 Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-ZHR / | ||||
#3: Chemical | ChemComp-CIT / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.1 M sodium citrate pH 5.9 and 26% (v/v) PEG 600. Protein buffer was 10 mM HEPES pH 8.0, 200 mM ammonium acetate buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.86→39.63 Å / Num. obs: 77756 / % possible obs: 99.7 % / Redundancy: 17.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.023 / Rrim(I) all: 0.098 / Net I/σ(I): 16 / Num. measured all: 1373660 / Scaling rejects: 761 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6CF9 Resolution: 1.86→39.63 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.513 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 122.08 Å2 / Biso mean: 37.588 Å2 / Biso min: 19.64 Å2
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Refinement step | Cycle: final / Resolution: 1.86→39.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.903 Å / Rfactor Rfree error: 0
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