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Yorodumi- PDB-7brf: Structure of NADH complex of Thermotoga maritima alpha-glucuronid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7brf | ||||||
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Title | Structure of NADH complex of Thermotoga maritima alpha-glucuronidase at 2.15 Angstrom resolution | ||||||
Components | Alpha-glucosidase, putative | ||||||
Keywords | HYDROLASE / hydrolase-oxidoreductase / alpha-glucuronidase activity / carbohydrate metabolism / NAD-binding Rossmann-fold / LDH C-terminal domain-like | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Manoj, N. / Mohapatra, S.B. | ||||||
Citation | Journal: To Be Published Title: Structure of NADH complex of Thermotoga maritima alpha-glucuronidase at 2.15 Angstrom resolution Authors: Manoj, N. / Mohapatra, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7brf.cif.gz | 285.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7brf.ent.gz | 232.2 KB | Display | PDB format |
PDBx/mmJSON format | 7brf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7brf_validation.pdf.gz | 731.8 KB | Display | wwPDB validaton report |
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Full document | 7brf_full_validation.pdf.gz | 735.4 KB | Display | |
Data in XML | 7brf_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 7brf_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/7brf ftp://data.pdbj.org/pub/pdb/validation_reports/br/7brf | HTTPS FTP |
-Related structure data
Related structure data | 1vjtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56911.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0752 / Plasmid: pMH2T7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Codon Plus RIL / References: UniProt: Q9WZL1 |
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#2: Chemical | ChemComp-NAI / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.54 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 12-18% PEG 3350, 0.2 M trilithium citrate, 0.1 M imidazole pH 5.8, 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2014 | |||||||||||||||||||||||||||
Radiation | Monochromator: Double Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.15→36.833 Å / Num. obs: 27625 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.36 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.073 / Rrim(I) all: 0.191 / Net I/σ(I): 8.1 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VJT Resolution: 2.15→36.833 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.13 / Details: Hydrogen atoms are included in riding positions
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.04 Å2 / Biso mean: 40.1634 Å2 / Biso min: 15.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→36.833 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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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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