+Open data
-Basic information
Entry | Database: PDB / ID: 1xn4 | ||||||
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Title | PUTATIVE MAR1 RIBONUCLEASE FROM LEISHMANIA MAJOR | ||||||
Components | ribonuclease MAR1 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / SGPP / PSI / Structural Genomics of Pathogenic Protozoa Consortium | ||||||
Function / homology | Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Ribonuclease mar1 Function and homology information | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å | ||||||
Authors | Caruthers, J. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily. Authors: Caruthers, J. / Zucker, F. / Worthey, E. / Myler, P.J. / Buckner, F. / Van Voorhuis, W. / Mehlin, C. / Boni, E. / Feist, T. / Luft, J. / Gulde, S. / Lauricella, A. / Kaluzhniy, O. / ...Authors: Caruthers, J. / Zucker, F. / Worthey, E. / Myler, P.J. / Buckner, F. / Van Voorhuis, W. / Mehlin, C. / Boni, E. / Feist, T. / Luft, J. / Gulde, S. / Lauricella, A. / Kaluzhniy, O. / Anderson, L. / Le Trong, I. / Holmes, M.A. / Earnest, T. / Soltis, M. / Hodgson, K.O. / Hol, W.G. / Merritt, E.A. | ||||||
History |
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Remark 999 | SEQUENCE This protein is a putative homologue of the MAR1 endoribonuclease from L tarentolae, SPTR ...SEQUENCE This protein is a putative homologue of the MAR1 endoribonuclease from L tarentolae, SPTR O77166. The closest Genbank sequence is the homologous protein from L Major, Genbank identifier LmjF12.0060. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xn4.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xn4.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xn4_validation.pdf.gz | 423 KB | Display | wwPDB validaton report |
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Full document | 1xn4_full_validation.pdf.gz | 423.9 KB | Display | |
Data in XML | 1xn4_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1xn4_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/1xn4 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/1xn4 | HTTPS FTP |
-Related structure data
Related structure data | 1x9gSC 1yzvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21615.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Plasmid details: SGPP target construct Lmaj001686AAA / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QGT7 |
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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: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 290 K / pH: 7.2 Details: 16% PEG 8000, 0.1 M K2HPO4, 0.1M MOPS pH7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20 |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 2294 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.126 |
Reflection shell | Resolution: 3.8→3.94 Å / Redundancy: 3.5 % / % possible all: 99.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X9G Resolution: 3.8→40.86 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.898 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R Free: 0.998 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.43 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→40.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.8→3.9 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 95.394 Å / Origin y: 22.306 Å / Origin z: 30.018 Å
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