+Open data
-Basic information
Entry | Database: PDB / ID: 3zwf | ||||||
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Title | Crystal structure of Human tRNase Z, short form (ELAC1). | ||||||
Components | ZINC PHOSPHODIESTERASE ELAC PROTEIN 1 | ||||||
Keywords | HYDROLASE / BETA-LACTAMASE / METAL-BINDING / TRNA PROCESSING / ZINC-BINDING / CATABOLISM | ||||||
Function / homology | Function and homology information : / tRNase Z / 3'-tRNA processing endoribonuclease activity / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Allerston, C.K. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Chaikuad, A. / Chalk, R. / Elkins, J.M. / Gileadi, C. / Latwiel, S.V.A. / Savitsky, P. ...Allerston, C.K. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Chaikuad, A. / Chalk, R. / Elkins, J.M. / Gileadi, C. / Latwiel, S.V.A. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Trnase Z, Short Form (Elac1). Authors: Allerston, C.K. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Chaikuad, A. / Chalk, R. / Elkins, J.M. / Gileadi, C. / Latwiel, S.V.A. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / ...Authors: Allerston, C.K. / Krojer, T. / Berridge, G. / Burgess-Brown, N. / Chaikuad, A. / Chalk, R. / Elkins, J.M. / Gileadi, C. / Latwiel, S.V.A. / Savitsky, P. / Vollmar, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zwf.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zwf.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/3zwf ftp://data.pdbj.org/pub/pdb/validation_reports/zw/3zwf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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) |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40720.887 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 3-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9H777, tRNase Z |
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-Non-polymers , 5 types, 299 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-NA / | #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 Å3/Da / Density % sol: 38.5 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 15% PEG 3350 0.2M NA NITRATE, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2011 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.57 Å / Num. obs: 67111 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 7.82 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 2 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MODEL DETERMINED FROM SIRAS EXPERIMENT Resolution: 1.7→72.81 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.175 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 133-151 196-242 317-346 362-446 DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.713 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→72.81 Å
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Refine LS restraints |
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