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Yorodumi- PDB-3zr4: STRUCTURAL EVIDENCE FOR AMMONIA TUNNELING ACROSS THE (BETA-ALPHA)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zr4 | ||||||
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Title | STRUCTURAL EVIDENCE FOR AMMONIA TUNNELING ACROSS THE (BETA-ALPHA)8 BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE BIENZYME COMPLEX | ||||||
Components |
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Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / L-histidine biosynthetic process / glutaminase activity / glutamine metabolic process / amino acid biosynthetic process / lyase activity / cytoplasm Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Vega, M.C. / Kuper, J. / Haeger, M.C. / Mohrlueder, J. / Marquardt, S. / Sterner, R. / Wilmanns, M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2012 Title: Catalysis Uncoupling in a Glutamine Amidotransferase Bienzyme by Unblocking the Glutaminase Active Site. Authors: List, F. / Vega, M.C. / Razeto, A. / Hager, M.C. / Sterner, R. / Wilmanns, M. #1: Journal: Structure / Year: 2002 Title: Structural Evidence for Ammonia Tunneling Across the (Beta Alpha)(8) Barrel of the Imidazole Glycerol Phosphate Synthase Bienzyme Complex. Authors: Douangamath, A. / Walker, M. / Beismann-Driemeyer, S. / Vega-Fernandez, M.C. / Sterner, R. / Wilmanns, M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zr4.cif.gz | 524.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zr4.ent.gz | 436.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zr4_validation.pdf.gz | 499.4 KB | Display | wwPDB validaton report |
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Full document | 3zr4_full_validation.pdf.gz | 535.5 KB | Display | |
Data in XML | 3zr4_validation.xml.gz | 52.1 KB | Display | |
Data in CIF | 3zr4_validation.cif.gz | 71.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/3zr4 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/3zr4 | HTTPS FTP |
-Related structure data
Related structure data | 2wjzC 1gpwS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 27753.871 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: RBSIISPHI-TMHISF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3310 / Variant (production host): DELTA-TRPEA2 References: UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases #2: Protein | Mass: 23130.564 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: RBSIISPHI-TMHISH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3310 / Variant (production host): DELTA-TRPEA2 References: UniProt: Q9X0C8, Transferases; Glycosyltransferases; Pentosyltransferases #3: Chemical | ChemComp-GOL / #4: Chemical | #5: 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: 2.35 Å3/Da / Density % sol: 47.6 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.802 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.802 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→55.95 Å / Num. obs: 51685 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / % possible all: 88.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GPW Resolution: 2.41→55.96 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.907 / SU B: 16.587 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.957 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→55.96 Å
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Refine LS restraints |
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