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Yorodumi- PDB-5z7h: Crystal structure of CcpE regulatory domain in citrate-bound form... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z7h | |||||||||
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Title | Crystal structure of CcpE regulatory domain in citrate-bound form from Staphyloccocus aureus | |||||||||
Components | LysR family transcriptional regulator | |||||||||
Keywords | TRANSCRIPTION / CcpE / complex / citrate-bound / Staphyloccocus aureus / transcriptional regulator | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | |||||||||
Authors | Chen, J. / Wang, L. / Shang, F. / Xu, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Citrate-responsive mechanism of catabolite control protein E from Staphyloccocus aureus Authors: Chen, J. / Wang, L. / Shang, F. / Xu, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z7h.cif.gz | 470.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z7h.ent.gz | 388.7 KB | Display | PDB format |
PDBx/mmJSON format | 5z7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z7h_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 5z7h_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 5z7h_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 5z7h_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/5z7h ftp://data.pdbj.org/pub/pdb/validation_reports/z7/5z7h | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 33280.230 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: The disordered residues and side chains were delated Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Gene: QU38_10390 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A0D1IHL7 #2: Chemical | ChemComp-FLC / #3: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4 M Sodium formate 10 mM Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9826 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9826 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 118067 / % possible obs: 93.2 % / Redundancy: 4.4 % / Rsym value: 0.152 / Net I/σ(I): 25.02 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.78 / Num. unique obs: 5336 / Rsym value: 0.774 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→31.889 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.44 / Phase error: 42.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→31.889 Å
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Refine LS restraints |
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LS refinement shell |
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