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Yorodumi- PDB-7mcb: Crystal structure of Staphylococcus aureus Cystathionine gamma ly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mcb | ||||||||||||
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Title | Crystal structure of Staphylococcus aureus Cystathionine gamma lyase Holoenzyme | ||||||||||||
Components | Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase | ||||||||||||
Keywords | LYASE / Amino-acid biosynthesis / Cysteine biosynthesis / Hydrogen sulfide production / PLP dependent enzyme | ||||||||||||
Function / homology | Function and homology information cystathionine gamma-synthase / : / cystathionine beta-lyase / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding ...cystathionine gamma-synthase / : / cystathionine beta-lyase / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||||||||
Authors | Nuthanakanti, A. / Serganov, A. / Kaushik, A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Science / Year: 2021 Title: Inhibitors of bacterial H 2 S biogenesis targeting antibiotic resistance and tolerance. Authors: Shatalin, K. / Nuthanakanti, A. / Kaushik, A. / Shishov, D. / Peselis, A. / Shamovsky, I. / Pani, B. / Lechpammer, M. / Vasilyev, N. / Shatalina, E. / Rebatchouk, D. / Mironov, A. / ...Authors: Shatalin, K. / Nuthanakanti, A. / Kaushik, A. / Shishov, D. / Peselis, A. / Shamovsky, I. / Pani, B. / Lechpammer, M. / Vasilyev, N. / Shatalina, E. / Rebatchouk, D. / Mironov, A. / Fedichev, P. / Serganov, A. / Nudler, E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mcb.cif.gz | 117 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mcb.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 7mcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mcb_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 7mcb_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 7mcb_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 7mcb_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/7mcb ftp://data.pdbj.org/pub/pdb/validation_reports/mc/7mcb | HTTPS FTP |
-Related structure data
Related structure data | 7mclC 7mcnC 7mcpC 7mcqC 7mctC 7mcuC 7mcyC 7md0C 7md1C 7md6C 7md8C 7md9C 7mdaC 7mdbC 4ixzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 41509.711 Da / Num. of mol.: 1 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: mccB, mccB_2, BTN44_10510, DD547_00421, DQV53_02590, EP54_01605, EQ90_13355, FA040_13395, G0X12_04165, G6Y10_12435, GO746_10250, GO803_10255, GO805_07485, GO821_10445, GO894_05080, GO942_04060, ...Gene: mccB, mccB_2, BTN44_10510, DD547_00421, DQV53_02590, EP54_01605, EQ90_13355, FA040_13395, G0X12_04165, G6Y10_12435, GO746_10250, GO803_10255, GO805_07485, GO821_10445, GO894_05080, GO942_04060, HMPREF2819_13610, HMPREF3211_01439, NCTC10654_00533, NCTC10702_00840, NCTC10988_00626, SAMEA1029528_01119, SAMEA1029547_02560, SAMEA1029553_00881, SAMEA103891286_02662, SAMEA1964876_02233, SAMEA1965205_02550, SAMEA1966505_02559, SAMEA1969349_02528, SAMEA1969845_00024, SAMEA1971706_00840, SAMEA1972827_00442, SAMEA2076212_02307, SAMEA2076218_02633, SAMEA2076220_02515, SAMEA2076226_02545, SAMEA2076463_02448, SAMEA2076464_02504, SAMEA2076470_02202, SAMEA2076472_02415, SAMEA2076478_01397, SAMEA2076480_02228, SAMEA2076481_02579, SAMEA2076743_02529, SAMEA2076745_00024, SAMEA2076746_01199, SAMEA2076747_02516, SAMEA2076749_02428, SAMEA2076751_02538, SAMEA2076752_00581, SAMEA2076755_02246, SAMEA2076756_02304, SAMEA2076758_02592, SAMEA2076759_02587, SAMEA2076761_00997, SAMEA2076762_02546, SAMEA2076763_01275, SAMEA2076764_00443, SAMEA2076765_02426, SAMEA2077023_00443, SAMEA2077025_02246, SAMEA2077027_02519, SAMEA2077029_02492, SAMEA2077031_02282, SAMEA2077034_02536, SAMEA2077035_00908, SAMEA2077039_00580, SAMEA2077040_02514, SAMEA2077041_00442, SAMEA2077044_02519, SAMEA2077045_01356, SAMEA2077046_02211, SAMEA2077293_01201, SAMEA2077294_01116, SAMEA2077295_02535, SAMEA2077297_02465, SAMEA2077300_00660, SAMEA2077301_02506, SAMEA2077302_01011, SAMEA2077303_02488, SAMEA2077307_02470, SAMEA2077832_02515, SAMEA2078252_01326, SAMEA2078256_02526, SAMEA2078307_01240, SAMEA2078308_02477, SAMEA2078553_02466, SAMEA2078558_00909, SAMEA2078560_01135, SAMEA2078569_01369, SAMEA2078570_02481, SAMEA2078572_01608, SAMEA2078824_02504, SAMEA2078837_01023, SAMEA2079048_02598, SAMEA2079051_01218, SAMEA2079277_01392, SAMEA2079291_02442, SAMEA2079503_01420, SAMEA2079507_02480, SAMEA2079512_02454, SAMEA2079517_02461, SAMEA2079724_02523, SAMEA2079727_02402, SAMEA2079728_02358, SAMEA2079732_00024, SAMEA2079946_02619, SAMEA2079949_02348, SAMEA2079951_02599, SAMEA2079952_00024, SAMEA2079957_00024, SAMEA2079958_00024, SAMEA2079960_02599, SAMEA2079961_02614, SAMEA2079968_02549, SAMEA2080329_00310, SAMEA2080330_00310, SAMEA2080334_02579, SAMEA2080433_00024, SAMEA2080812_02589, SAMEA2080898_01599, SAMEA2080900_02516, SAMEA2080904_02530, SAMEA2080913_02537, SAMEA2081043_02522, SAMEA2081053_02264, SAMEA2081054_02235, SAMEA2081055_02550, SAMEA2081060_02563, SAMEA2081211_02363, SAMEA2081213_02446, SAMEA2081218_00838, SAMEA2081341_02527, SAMEA2081342_02593, SAMEA2081349_02540, SAMEA2081359_02598, SAMEA2081362_00464, SAMEA2081468_01079, SAMEA2081474_00910, SAMEA2081475_02534, SAMEA2081476_02404, SAMEA2081479_00996, SAMEA2081480_00533, SAMEA2081560_02486, SAMEA2081561_02504, SAMEA2081564_01449, SAMEA2081567_02515, SAMEA2081568_01446, SAMEA2081569_02545, SAMEA2081570_01449, SAMEA2081571_01216, SAMEA2081572_02471, SAMEA2081573_02217, SAMEA2081575_00580, SAMEA2081577_01158, SAMEA2081578_02511, SAMEA2081579_02531, SAMEA2081581_02162, SAMEA2081582_02344, SAMEA2081673_02599, SAMEA2081674_02397, SAMEA4008573_02705, SAMEA4008676_02295, SAMEA70146418_02721, SAMEA958766_00501, SAMEA958770_02469, SAMEA958772_00350, SAMEA958778_00586, SAMEA958779_02116, SAMEA958785_02543, SAMEA958793_02555, SAMEA958798_02471, SAMEA958804_02558, SAMEA958810_02365, SAMEA958836_00976, SAMEA958838_01939, SAMEA958845_00024, SAMEA958846_02565, SAMEA958848_02402, SAMEA958855_02196, SAMEA958858_00594, SAMEA958898_01850, SAMEA958906_02198, SAMEA958924_02531, SAMEA958925_02436, SAMEA958951_01115, SAMEA958953_00350, SAMEA958961_02116, SAMEA958979_00024, SAMEA958987_02419, SAMEA958995_02394 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: X5E0F1, cystathionine gamma-lyase, cystathionine beta-lyase, cystathionine gamma-synthase | ||||||
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#2: Chemical | ChemComp-PLP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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 grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M HEPES , pH 7.6 1.4 M Tri sodium Citrate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→30 Å / Num. obs: 45133 / % possible obs: 99.8 % / Redundancy: 18.7 % / Biso Wilson estimate: 36.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.14→2.19 Å / Redundancy: 18.1 % / Num. unique obs: 3211 / CC1/2: 0.955 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IXZ Resolution: 2.14→29.39 Å / SU ML: 0.1632 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.3738 / Stereochemistry target values: 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: 42.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→29.39 Å
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Refine LS restraints |
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LS refinement shell |
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