+Open data
-Basic information
Entry | Database: PDB / ID: 4gyr | ||||||
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Title | Granulibacter bethesdensis allophanate hydrolase apo | ||||||
Components | Allophanate hydrolase | ||||||
Keywords | HYDROLASE / Amidase signature family enzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Granulibacter bethesdensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Lin, Y. / St Maurice, M. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family. Authors: Lin, Y. / St Maurice, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gyr.cif.gz | 186.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gyr.ent.gz | 145 KB | Display | PDB format |
PDBx/mmJSON format | 4gyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gyr_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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Full document | 4gyr_full_validation.pdf.gz | 478.6 KB | Display | |
Data in XML | 4gyr_validation.xml.gz | 37 KB | Display | |
Data in CIF | 4gyr_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/4gyr ftp://data.pdbj.org/pub/pdb/validation_reports/gy/4gyr | HTTPS FTP |
-Related structure data
Related structure data | 4gysSC 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | The biological unit consists of chain A from Sym ID 6_565 and chain B from the identity matrix (Sym ID 1_555) |
-Components
#1: Protein | Mass: 66537.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Granulibacter bethesdensis (bacteria) / Strain: ATCC BAA-1260 / CGDNIH1 / Gene: GbCGDNIH1_1744 / Plasmid: pET28a-(HIS)8-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q0BRB0, allophanate hydrolase #2: 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: 2.63 Å3/Da / Density % sol: 53.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 24%(w/v)PEG4000,50mM MgCl2,100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 33600 / Num. obs: 33519 / % possible obs: 99.9 % / Redundancy: 9 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 18.1 / Num. unique all: 1634 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GYS Resolution: 2.8→40.045 Å / SU ML: 0.88 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 30.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.529 Å2 / ksol: 0.307 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→40.045 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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