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Yorodumi- PDB-3m1r: The crystal structure of formimidoylglutamase from Bacillus subti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m1r | ||||||
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Title | The crystal structure of formimidoylglutamase from Bacillus subtilis subsp. subtilis str. 168 | ||||||
Components | Formimidoylglutamase | ||||||
Keywords | HYDROLASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Histidine metabolism / Manganese / Metal-binding | ||||||
Function / homology | Function and homology information formimidoylglutamase / formimidoylglutamase activity / putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / manganese ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.199 Å | ||||||
Authors | Tan, K. / Bigelow, L. / Trevino, D. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of formimidoylglutamase from Bacillus subtilis subsp. subtilis str. 168 Authors: Tan, K. / Bigelow, L. / Buck, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m1r.cif.gz | 746 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m1r.ent.gz | 644.5 KB | Display | PDB format |
PDBx/mmJSON format | 3m1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m1r_validation.pdf.gz | 522.5 KB | Display | wwPDB validaton report |
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Full document | 3m1r_full_validation.pdf.gz | 583.5 KB | Display | |
Data in XML | 3m1r_validation.xml.gz | 74.3 KB | Display | |
Data in CIF | 3m1r_validation.cif.gz | 99.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/3m1r ftp://data.pdbj.org/pub/pdb/validation_reports/m1/3m1r | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 35756.176 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: str. 168 / Gene: hutG, BSU39380, EE57C / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: P42068, formimidoylglutamase |
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-Non-polymers , 5 types, 299 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-PEG / #5: Chemical | #6: 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: 2.43 Å3/Da / Density % sol: 49.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M MgCl2, 0.1M Sodium cacodylate, 50% (v/v) PEG200, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 19, 2009 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→32.5 Å / Num. all: 102844 / Num. obs: 102844 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 7 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5103 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.199→32.474 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 24.09 / 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 / Bsol: 60.229 Å2 / ksol: 0.379 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.199→32.474 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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