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Yorodumi- PDB-1lrt: CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lrt | ||||||
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Title | CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME | ||||||
Components | INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / ternary complex / alpha-beta barrel / flexible loop / flap | ||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / protein-containing complex / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Tritrichomonas foetus (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Gan, L. / Petsko, G.A. / Hedstrom, L. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Crystal structure of a ternary complex of Tritrichomonas foetus inosine 5'-monophosphate dehydrogenase: NAD+ orients the active site loop for catalysis Authors: Gan, L. / Petsko, G.A. / Hedstrom, L. | ||||||
History |
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Remark 999 | SEQUENCE AUTHOR STATES THE WILD TYPE T. FOETUS IMPDH CONSISTS OF 503 RESIDUES, HOWEVER THEIR ...SEQUENCE AUTHOR STATES THE WILD TYPE T. FOETUS IMPDH CONSISTS OF 503 RESIDUES, HOWEVER THEIR PROTEIN WAS A MUTANT OFIMPDH. RESIDUES 101-226 IN THE SUBDOMAIN WERE DELETED BECAUSE IT IS NOT REQUIRED FOR IMPDH ACTIVITY. ACCORDING TO THE AUTHORS THE SUBDOMAIN WAS DELETED IN THIS CONSTRUCT TO FACILITATE CRYSTALLIZATION AND THERE IS NO EXOGENOUS LINKER BETWEEN THE RESIDUES 100 AND 227. AUTHOR ALSO STATES ALTHOUGH RESIDUE 279 IS GLU IN SWISS DATABANK, BOTH SEQUENCING RESULT AND ELECTRON DENSITY OF THE STRUCTURE SHOW RESIDUE 279 AS ASP IN THEIR PROTEIN. THE AUTHOR SUGGEST A CONSERVED MUTATION OCCURS AFTER THE CDNA OF THE ENZYME GENE IS TRANSFORMED INTO E. COLI. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lrt.cif.gz | 282.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lrt.ent.gz | 231.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lrt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lrt_validation.pdf.gz | 942.4 KB | Display | wwPDB validaton report |
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Full document | 1lrt_full_validation.pdf.gz | 986 KB | Display | |
Data in XML | 1lrt_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 1lrt_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lrt ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lrt | HTTPS FTP |
-Related structure data
Related structure data | 1ak5S 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
-Protein / Sugars , 2 types, 6 molecules ABCD
#1: Protein | Mass: 41198.891 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tritrichomonas foetus (eukaryote) / Gene: IMPDH / Plasmid: pKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): H712 / References: UniProt: P50097, IMP dehydrogenase #2: Sugar | |
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-Non-polymers , 5 types, 567 molecules
#3: Chemical | ChemComp-K / #4: Chemical | ChemComp-IMP / #5: Chemical | ChemComp-TAD / #6: Chemical | ChemComp-TRS / #7: 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: 2.72 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: PEG 10,000, MES, glycerol, potassium chloride, beta-octylglucoside, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 87015 / Num. obs: 82096 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.4 / Num. unique all: 8087 / Rsym value: 0.398 / % possible all: 91.3 |
Reflection | *PLUS Num. obs: 87015 / % possible obs: 96.8 % / Num. measured all: 356029 |
Reflection shell | *PLUS % possible obs: 91.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AK5 Resolution: 2.2→29.86 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 392538.27 / Data cutoff high rms absF: 392538.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.6917 Å2 / ksol: 0.421356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.86 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection obs: 71997 / Num. reflection Rfree: 8033 / Rfactor Rwork: 0.218 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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