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Yorodumi- PDB-1tc2: TERNARY SUBSTRATE COMPLEX OF THE HYPOXANTHINE PHOSPHORIBOSYLTRANS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tc2 | ||||||
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Title | TERNARY SUBSTRATE COMPLEX OF THE HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE FROM TRYPANOSOMA CRUZI | ||||||
Components | PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE) | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / NUCLEOTIDE METABOLISM / PURINE SALVAGE / TERNARY COMPLEX / NEAR TRANSITION STATE | ||||||
Function / homology | Function and homology information hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Focia, P.J. / Craig III, S.P. / Eakin, A.E. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Approaching the transition state in the crystal structure of a phosphoribosyltransferase. Authors: Focia, P.J. / Craig III, S.P. / Eakin, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tc2.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tc2.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tc2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1tc2_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1tc2_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1tc2_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/1tc2 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/1tc2 | HTTPS FTP |
-Related structure data
Related structure data | 1tc1S 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.865547, 0.408421, 0.289862), Vector: |
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 25595.404 Da / Num. of mol.: 2 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, 199 molecules
#2: Chemical | #3: Chemical | #5: Chemical | ChemComp-MN / | #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: 2.03 Å3/Da / Density % sol: 39.35 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging 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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→20.6 Å / Num. obs: 33026 / % possible obs: 88.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.051 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.81→1.85 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.32 / % possible all: 80.1 |
Reflection | *PLUS Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 80.1 % / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TC1 Resolution: 1.81→6 Å / Cross valid method: THROUGHOUT / σ(F): 1 Details: PATCH STATEMENTS WERE USED FOR CIS PEPTIDES AND METAL-OXYGEN BONDS SER 88 IS POORLY ORDERED IN SUBUNIT A THE ENERGIES FOR METAL-OXYGEN BOND LENGTHS AND ANGLES WERE SET ARTIFICIALLY LOW ...Details: PATCH STATEMENTS WERE USED FOR CIS PEPTIDES AND METAL-OXYGEN BONDS SER 88 IS POORLY ORDERED IN SUBUNIT A THE ENERGIES FOR METAL-OXYGEN BOND LENGTHS AND ANGLES WERE SET ARTIFICIALLY LOW DURING REFINEMENT IN ORDER TO ALLOW THESE ATOMS MORE FREEDOM TO ADJUST
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Refinement step | Cycle: LAST / Resolution: 1.81→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.85 Å / Total num. of bins used: 15
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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