+Open data
-Basic information
Entry | Database: PDB / ID: 4g3h | ||||||
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Title | Crystal structure of helicobacter pylori arginase | ||||||
Components | Arginase (RocF) | ||||||
Keywords | HYDROLASE / arginase / Rossmann Fold / Hydrolytic enzyme / manganous ion binding / Hydrolysis | ||||||
Function / homology | Function and homology information arginase / arginase activity / arginine catabolic process to ornithine / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zhang, J. / Zhang, X. / Li, D. / Hu, Y. / Zou, Q. / Wang, D. | ||||||
Citation | Journal: To be Published Title: Structure and function studies on Helicobacter pylori arginase Authors: Zhang, J. / Zhang, X. / Li, D. / Hu, Y. / Zou, Q. / Wang, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g3h.cif.gz | 265.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g3h.ent.gz | 213.9 KB | Display | PDB format |
PDBx/mmJSON format | 4g3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g3h_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 4g3h_full_validation.pdf.gz | 505.8 KB | Display | |
Data in XML | 4g3h_validation.xml.gz | 55 KB | Display | |
Data in CIF | 4g3h_validation.cif.gz | 76.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/4g3h ftp://data.pdbj.org/pub/pdb/validation_reports/g3/4g3h | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38051.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_1399 / Production host: Escherichia coli (E. coli) / References: UniProt: O25949 #2: Chemical | ChemComp-MN / #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: 2.36 Å3/Da / Density % sol: 47.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% polyethylene glycol 3350, 100mM Bis-Tris pH 5.5, 1mM MnCl2, 15mM guanidine hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→34.918 Å / Num. all: 73851 / Num. obs: 66320 / % possible obs: 89.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % |
Reflection shell | Highest resolution: 2.2 Å / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.9 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 74.8104 Å2 | ||||||||||||||||||||
Displacement parameters | Biso max: 158.78 Å2 / Biso mean: 36.3794 Å2 / Biso min: 7.25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→34.9 Å
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Refine LS restraints |
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Xplor file |
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