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Yorodumi- PDB-1qmh: Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiqui... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qmh | ||||||
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Title | Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology | ||||||
Components | RNA 3'-TERMINAL PHOSPHATE CYCLASE | ||||||
Keywords | LIGASE / 2'3'CYCLIC PHOSPHATE RNA | ||||||
Function / homology | Function and homology information RNA 3'-terminal-phosphate cyclase (ATP) / RNA-3'-phosphate cyclase activity / RNA processing / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Palm, G.J. / Billy, E. / Filipowicz, W. / Wlodawer, A. | ||||||
Citation | Journal: Structure / Year: 2000 Title: Crystal Structure of RNA 3'-Terminal Phosphate Cyclase, a Ubiquitous Enzyme with Unusual Topology Authors: Palm, G.J. / Billy, E. / Filipowicz, W. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qmh.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qmh.ent.gz | 114.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qmh_validation.pdf.gz | 476.7 KB | Display | wwPDB validaton report |
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Full document | 1qmh_full_validation.pdf.gz | 505.6 KB | Display | |
Data in XML | 1qmh_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 1qmh_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/1qmh ftp://data.pdbj.org/pub/pdb/validation_reports/qm/1qmh | HTTPS FTP |
-Related structure data
Related structure data | 1qmiSC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.515842, -0.671843, -0.531539), Vector: |
-Components
#1: Protein | Mass: 37014.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Cellular location: CYTOPLASM / Gene: RTCA / Plasmid: PET-11D_ECOLI CYCLASE / Cellular location (production host): CYTOPLASM / Gene (production host): RTCA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P46849, RNA 3'-terminal-phosphate cyclase (ATP) #2: Chemical | #3: Chemical | ChemComp-DTO / | #4: Water | ChemComp-HOH / | Sequence details | C-TERMINAL HIS TAG ADDED | |
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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: 2.84 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: THE PROTEIN WAS CRYSTALLIZED FROM 13-15% MPEG 2000, 200 MM NA-CITRATE PH 4.0, 200 MM TRIS/HCL PH 8.0, 2 MM DTT. PROTEIN CONCENTRATION WAS CA. 15 MG/ML. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.96456 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96456 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 50057 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.043 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.268 / % possible all: 83.4 |
Reflection | *PLUS Num. measured all: 159690 / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 83.4 % / Rmerge(I) obs: 0.268 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QMI, CHAIN A Resolution: 2.1→10 Å / SU B: 5.47 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.215 Details: REFINEMENT WAS STARTED WITH XPLOR 3.1, THE HIS TAG OF CHAINS A AND B WERE NOT VISIBLE IN THE ELECTRON DENSITY. THE ELECTRON DENSITY AROUND RESIDUES 94 TO 97 COULD NOT BE MODELLED WITH STANDARD BACKBONE GEOMETRY.
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Displacement parameters | Biso mean: 37.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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