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Yorodumi- PDB-5ahl: Apo-form of the DeltaCBS mutant of IMPDH from Pseudomonas aeruginosa -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ahl | ||||||
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Title | Apo-form of the DeltaCBS mutant of IMPDH from Pseudomonas aeruginosa | ||||||
Components | INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / CBS MODULE / DELETION MUTANT / ALLOSTERIC REGU NUCLEOTIDE METABOLISM | ||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / ATP binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å | ||||||
Authors | Labesse, G. / Alexandre, T. / Gelin, M. / Haouz, A. / Munier-Lehmann, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Crystallographic Studies of Two Variants of Pseudomonas Aeruginosa Impdh with Impaired Allosteric Regulation Authors: Labesse, G. / Alexandre, T. / Gelin, M. / Haouz, A. / Munier-Lehmann, H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ahl.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ahl.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ahl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ahl_validation.pdf.gz | 425 KB | Display | wwPDB validaton report |
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Full document | 5ahl_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 5ahl_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 5ahl_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/5ahl ftp://data.pdbj.org/pub/pdb/validation_reports/ah/5ahl | HTTPS FTP |
-Related structure data
Related structure data | 5ahmC 5ahnC 4dqwS C: citing same article (ref.) 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: 41702.574 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-92,202-489 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXM5, IMP dehydrogenase |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Sequence details | DELETION MUTANT (RESIDUES 93-201) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | Details: HEPES 0.1 M PH 7.5, NACL 4.3 M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→82.2 Å / Num. obs: 45333 / % possible obs: 100 % / Observed criterion σ(I): 1.1 / Redundancy: 14.7 % / Biso Wilson estimate: 23.01 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.89→1.98 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DQW Resolution: 1.951→45.476 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 20.22 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.951→45.476 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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