+Open data
-Basic information
Entry | Database: PDB / ID: 7rw3 | ||||||
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Title | E. coli cysteine desulfurase SufS N99D | ||||||
Components | Cysteine desulfurase | ||||||
Keywords | TRANSFERASE / cysteine desulfurase / SufS / PLP | ||||||
Function / homology | Function and homology information selenocysteine lyase / selenocysteine lyase activity / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Dunkle, J.A. / Gogar, R. / Frantom, P.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: The beta-latch structural element of the SufS cysteine desulfurase mediates active site accessibility and SufE transpersulfurase positioning. Authors: Gogar, R.K. / Carroll, F. / Conte, J.V. / Nasef, M. / Dunkle, J.A. / Frantom, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rw3.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rw3.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rw3_validation.pdf.gz | 769.8 KB | Display | wwPDB validaton report |
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Full document | 7rw3_full_validation.pdf.gz | 770.8 KB | Display | |
Data in XML | 7rw3_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 7rw3_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/7rw3 ftp://data.pdbj.org/pub/pdb/validation_reports/rw/7rw3 | HTTPS FTP |
-Related structure data
Related structure data | 7rujC 6mr2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44513.645 Da / Num. of mol.: 1 / Mutation: N99D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: sufS, AM464_26295, AUQ13_12030, BANRA_00144, BANRA_00498, BUE81_02100, BvCms2454_03222, BvCmsHHP056_00376, BvCmsKKP036_02154, BvCmsKSP026_00913, BW690_21095, C2U48_26455, C3F40_02340, C5F72_ ...Gene: sufS, AM464_26295, AUQ13_12030, BANRA_00144, BANRA_00498, BUE81_02100, BvCms2454_03222, BvCmsHHP056_00376, BvCmsKKP036_02154, BvCmsKSP026_00913, BW690_21095, C2U48_26455, C3F40_02340, C5F72_12470, C5F73_16550, CA593_19565, CI694_12360, D0X26_02680, D3821_13970, D9D44_08095, D9I97_06950, D9J52_00990, DJ503_04985, DT034_04565, E2119_03595, E4K51_04160, E4K53_02750, E4K55_02210, EA213_01125, EAI52_07715, EC3234A_33c01830, ECTO6_02268, EEP23_12650, EI021_02920, EI041_09080, EIZ93_02005, EL75_1975, EL79_2015, ETECE1441_02263, ETECE925_02258, EYD11_10615, EYV18_16700, F1E19_09770, F9X20_017695, F9X20_17865, FKC84_00740, FRV13_11320, FV293_04975, G5688_08175, G5696_08550, GHD50_00995, GKF86_07510, GKF89_05190, GQE33_02870, GQE34_20940, GQE67_02970, GRW02_06095, GRW05_00495, GRW57_07250, GRW81_10520, H4P50_11345, H4P51_11710, HH707_000397, HLT96_01805, HLU13_01505, HMQ05_01935, HNN86_11820, HNO08_06140, HNV44_03825, HV065_07405, HVV53_04920, HVX22_10640, HVX24_10540, HVY79_11755, HVY93_10710, HVZ24_10295, HX136_13565, NCTC10429_03516, NCTC13148_01082, NCTC8500_02620, NCTC9045_02773, NCTC9062_00321, NCTC9073_05651, RK56_009090, SAMEA3472047_04360, SAMEA3472080_01352, SAMEA3484427_00841, SAMEA3484429_00952, SAMEA3752559_02324, SAMEA3753300_02697, SK85_01902, WP2S18E08_22360, WP7S17E04_19980 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A090LEQ9, cysteine desulfurase, selenocysteine lyase |
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#2: Chemical | ChemComp-PLP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6 Å3/Da / Density % sol: 80 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 4-4.5M NaCl, 100 mM MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 12, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→39.45 Å / Num. obs: 48187 / % possible obs: 98.8 % / Redundancy: 9.911 % / Biso Wilson estimate: 40.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.086 / Χ2: 0.904 / Net I/σ(I): 22.99 / Num. measured all: 477586 / Scaling rejects: 1290 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdbid 6mr2 Resolution: 2.3→39.45 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.63 / 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: 109.12 Å2 / Biso mean: 42.1316 Å2 / Biso min: 25.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→39.45 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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