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Yorodumi- PDB-7r8q: Closed form of SAOUHSC_02373 in complex with ADP, citrate, Mg2+ a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r8q | ||||||
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Title | Closed form of SAOUHSC_02373 in complex with ADP, citrate, Mg2+ and Na+ | ||||||
Components | ATP-grasp domain-containing protein | ||||||
Keywords | LIGASE / ATP-grasp superfamily / L-amino acid ligase | ||||||
Function / homology | ATP-grasp fold / ATP-grasp fold profile. / ATP binding / metal ion binding / ADENOSINE-5'-DIPHOSPHATE / CITRIC ACID / ATP-grasp domain-containing protein Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Pederick, J.L. / Bruning, J.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Discovery of an ʟ-amino acid ligase implicated in Staphylococcal sulfur amino acid metabolism. Authors: Pederick, J.L. / Horsfall, A.J. / Jovcevski, B. / Klose, J. / Abell, A.D. / Pukala, T.L. / Bruning, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r8q.cif.gz | 183.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r8q.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 7r8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r8q_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7r8q_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7r8q_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 7r8q_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/7r8q ftp://data.pdbj.org/pub/pdb/validation_reports/r8/7r8q | HTTPS FTP |
-Related structure data
Related structure data | 7r8pSC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46930.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_02373 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2FWC5 |
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-Non-polymers , 5 types, 455 molecules
#2: Chemical | ChemComp-CIT / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate tribasic dihydrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2→36.89 Å / Num. obs: 64488 / % possible obs: 98.7 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.056 / Rrim(I) all: 0.148 / Net I/σ(I): 9 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.6 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7R8P Resolution: 2→36.89 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.67 / 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: 96.09 Å2 / Biso mean: 40.4317 Å2 / Biso min: 23.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→36.89 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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