[English] 日本語
Yorodumi- PDB-1d1u: USE OF AN N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d1u | ||||||
---|---|---|---|---|---|---|---|
Title | USE OF AN N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE TO FACILITATE CRYSTALLIZATION AND ANALYSIS OF A PSEUDO-16-MER DNA MOLECULE CONTAINING G-A MISPAIRS | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / G-A MISPAIR / SYN-ADENINE / NUCLEIC ACID / PROTEIN-DNA COMPLEX / SINGLE-STRAND OVERHANG / REVERSE TRANSCRIPTASE / MOLONEY MURINE LEUKEMIA VIRUS / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Moloney murine leukemia virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Cote, M.L. / Yohannan, S. / Georgiadis, M.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs. Authors: Cote, M.L. / Yohannan, S.J. / Georgiadis, M.M. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Crystal Structures of the N-Terminal Fragment from Moloney Murine Leukemia Virus Reverse Transcriptase Complexed with Nucleic Acid: Functional Implications for Template-Primer Binding to the Fingers Domain Authors: Najmudin, S. / Cote, M.L. / Sun, D. / Yohannan, S. / Montano, S.P. / Gu, J. / Georgiadis, M.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1d1u.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1d1u.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 1d1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d1u ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d1u | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC |
---|---|
#2: DNA chain | Mass: 3079.031 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE SEQUENCE 5'-CTCGTG-3' WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS 392 DNA/RNA SYNTHESIZER |
#3: Protein | Mass: 28934.287 Da / Num. of mol.: 1 / Fragment: FINGERS AND PALM DOMAIN OF MMLV RT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Gene: MMLV REVERSE TRANSCRIPTASE / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, DNA-directed DNA polymerase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.98 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 108 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 17117 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.278 / % possible all: 98.5 |
Reflection shell | *PLUS % possible obs: 98.5 % / Mean I/σ(I) obs: 4.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: MODEL WAS REFINED WITH TWO DIFFERENT SIDE-CHAIN CONFORMATIONS FOR TYR 64 (IN THE A MOLECULE). BOTH WERE HELD AT 50% OCCUPANCY. THE 5'- TERMINAL ADENINE OF THE "C" CHAIN MAY HAVE EITHER THE ...Details: MODEL WAS REFINED WITH TWO DIFFERENT SIDE-CHAIN CONFORMATIONS FOR TYR 64 (IN THE A MOLECULE). BOTH WERE HELD AT 50% OCCUPANCY. THE 5'- TERMINAL ADENINE OF THE "C" CHAIN MAY HAVE EITHER THE SYN- OR ANTI- CONFORMATION. THE DEPOSITED DATA HAVE ADENINE C7 IN THE ANTI- CONFORMATION. INDEPENDENT REFINEMENTS OF THE STRUCTURAL MODEL WITH EITHER A SYN- OR AN ANTI-CONFORMATION FOR THE 5'-TERMINAL ADENINE ((A7) IN THE "C" CHAIN) YIELDED ELECTRON DENSITY MAPS WHICH GAVE NO PREFERENCE FOR ONE CONFORMATION OVER THE OTHER, AND NO INDICATION OF PARTIAL OCCUPANCIES FOR BOTH. THE INDEPENDENT REFINEMENTS YIELDED THE SAME REFINEMENT STATISTICS. THE DEPOSITED DATA CONTAIN THE ADENINE (A7) IN THE ANTI-CONFORMATION. THE COORDINATES FOR THE SYN-ADENINE ARE AVAILABLE UPON REQUEST FROM THE AUTHORS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|