+Open data
-Basic information
Entry | Database: PDB / ID: 1i13 | ||||||
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Title | ANALYSIS OF AN INVARIANT ASPARTIC ACID IN HPRTS-ALANINE MUTANT | ||||||
Components | HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / NUCLEOTIDE METABOLISM / PURINE SALVAGE / TERNARY COMPLEX / CATALYTIC BASE | ||||||
Function / homology | Function and homology information hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Canyuk, B. / Focia, P.J. / Eakin, A.E. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: The role for an invariant aspartic acid in hypoxanthine phosphoribosyltransferases is examined using saturation mutagenesis, functional analysis, and X-ray crystallography. Authors: Canyuk, B. / Focia, P.J. / Eakin, A.E. #1: Journal: Biochemistry / Year: 1998 Title: Approaching the Transition State in the Crystal Structure of a Phosphoribosyltransferase Authors: Focia, P.J. / Craig, S.P. / Eakin, A.E. | ||||||
History |
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Remark 999 | SEQUENCE THIS HPRT WAS CLONED FROM A DIFFERENT STRAIN OF TRYPANOSOMA CRUZI AND VARIES FROM A ...SEQUENCE THIS HPRT WAS CLONED FROM A DIFFERENT STRAIN OF TRYPANOSOMA CRUZI AND VARIES FROM A PREVIOUSLY REPORTED SEQUENCE AT LYS 23, CYS 66 AND LEU 86. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i13.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i13.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i13 ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i13 | HTTPS FTP |
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-Related structure data
Related structure data | 1i0iC 1i0lC 1i14C 1tc2S 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 25480.316 Da / Num. of mol.: 2 / Mutation: M23K, S66C, V86L, D115A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: Q27796, UniProt: Q4DRC4*PLUS, hypoxanthine phosphoribosyltransferase #4: Sugar | |
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-Non-polymers , 4 types, 185 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #5: Chemical | ChemComp-FMT / | #6: 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: 2.05 Å3/Da / Density % sol: 40.06 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 6000, Sodium acetate, ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 1999 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→30 Å / Num. obs: 36405 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.3 / % possible all: 92.5 |
Reflection | *PLUS Num. obs: 33269 |
Reflection shell | *PLUS Highest resolution: 1.84 Å / Lowest resolution: 1.89 Å / % possible obs: 93.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1tc2 with ligands, water molecules and loop II removed Resolution: 1.84→6 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: PATCH STATEMENTS WERE USED FOR CIS PEPTIDES AND METAL-OXYGEN BONDS
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Refinement step | Cycle: LAST / Resolution: 1.84→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.84 Å / Total num. of bins used: 15
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Xplor file |
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Refinement | *PLUS Rfactor all: 0.25 / Rfactor obs: 0.192 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.271 |