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- PDB-7l0a: Crystal structure of s-formylglutathione hydrolase (FrmB) from St... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l0a | ||||||||||||
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Title | Crystal structure of s-formylglutathione hydrolase (FrmB) from Staphylococcus aureus, apoenzyme | ||||||||||||
![]() | Esterase family protein | ||||||||||||
![]() | HYDROLASE / FrmB | ||||||||||||
Function / homology | ![]() S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Miller, J.J. / Jez, J.M. / Odom John, A.R. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-guided microbial targeting of antistaphylococcal prodrugs. Authors: Miller, J.J. / Shah, I.T. / Hatten, J. / Barekatain, Y. / Mueller, E.A. / Moustafa, A.M. / Edwards, R.L. / Dowd, C.S. / Planet, P.J. / Muller, F.L. / Jez, J.M. / Odom John, A.R. #1: ![]() Title: Structure-guided microbial targeting of antistaphylococcal prodrugs Authors: Miller, J.J. / Shah, I.T. / Hatten, J. / Barekatain, Y. / Mueller, E.A. / Moustafa, A.M. / Edwards, R.L. / Dowd, C.S. / Planet, P.J. / Muller, F.L. / Jez, J.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 | ![]() | 301.6 KB | Display | ![]() |
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PDB format | ![]() | 248.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.1 KB | Display | ![]() |
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Full document | ![]() | 437.3 KB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l0bC ![]() 4rgyS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29931.725 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DD547_02660, DQV53_15175, EP54_00010, EQ90_02595, G0V24_06825, G0Z18_09875, G6Y10_06490, GO746_05055, GO803_04470, GO805_09630, GO821_02780, GO894_07900, GO942_11740, HMPREF2819_04260, ...Gene: DD547_02660, DQV53_15175, EP54_00010, EQ90_02595, G0V24_06825, G0Z18_09875, G6Y10_06490, GO746_05055, GO803_04470, GO805_09630, GO821_02780, GO894_07900, GO942_11740, HMPREF2819_04260, HMPREF3211_01237, NCTC10654_02801, NCTC10702_04070, NCTC10988_03042, RK64_00235 Production host: ![]() ![]() References: UniProt: A0A0D6GS23, UniProt: Q2FUY3*PLUS, S-formylglutathione hydrolase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 20 uL hanging drops containing a 1:1 mixture of protein (6 mg/mL) and crystallization buffer (0.1 M Tricine pH 7.7, 15% PEG6K, 2.5 M NaCl, 0.125% n-dodecyl-B-D-glucoside) |
-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: Feb 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 78193 / % possible obs: 96.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.054 / Rrim(I) all: 0.093 / Χ2: 2.643 / Net I/σ(I): 11.7 / Num. measured all: 217757 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.415 / Num. unique obs: 3961 / CC1/2: 0.992 / Rpim(I) all: 0.034 / Rrim(I) all: 0.059 / Χ2: 3.02 / % possible all: 99.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RGY Resolution: 1.6→36.81 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.36 / 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: 114.29 Å2 / Biso mean: 27.79 Å2 / Biso min: 10.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→36.81 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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