+Open data
-Basic information
Entry | Database: PDB / ID: 1sen | ||||||
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Title | Endoplasmic reticulum protein Rp19 O95881 | ||||||
Components | Thioredoxin-like protein p19 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Endoplasmic reticulum / Rp19 / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | Function and homology information protein-disulfide reductase (glutathione) / protein-disulfide reductase (glutathione) activity / protein-disulfide reductase activity / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum lumen / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.199 Å | ||||||
Authors | Liu, Z.-J. / Chen, L. / Tempel, W. / Shah, A. / Lee, D. / Dailey, T.A. / Mayer, M.R. / Rose, J.P. / Richardson, D.C. / Richardson, J.S. ...Liu, Z.-J. / Chen, L. / Tempel, W. / Shah, A. / Lee, D. / Dailey, T.A. / Mayer, M.R. / Rose, J.P. / Richardson, D.C. / Richardson, J.S. / Dailey, H.A. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be Published Title: Endoplasmic reticulum protein Rp19 Authors: Liu, Z.-J. / Chen, L. / Tempel, W. / Shah, A. / Lee, D. / Rose, J.P. / Richardson, D.C. / Richardson, J.S. / Wang, B.-C. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1997 Title: Refinement of Macromolecular Structures by the Maximum-Likelihood Method Authors: Murshudov, G.N. / Vagin, A.A. / Dodson, E.J. #2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1999 Title: Automated MAD and MIR structure solution Authors: Terwilliger, T.C. / Berendzen, J. #3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2000 Title: Maximum likelihood density modification Authors: Terwilliger, T.C. #4: Journal: Nat.Struct.Biol. / Year: 1999 Title: Automated protein model building combined with iterative structure refinement Authors: Perrakis, A. / Morris, R. / Lamzin, V.S. | ||||||
History |
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Remark 300 | BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sen.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sen.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 1sen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sen_validation.pdf.gz | 420.3 KB | Display | wwPDB validaton report |
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Full document | 1sen_full_validation.pdf.gz | 420.6 KB | Display | |
Data in XML | 1sen_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1sen_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/1sen ftp://data.pdbj.org/pub/pdb/validation_reports/se/1sen | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 18304.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: The protein was cloned, expressed and purified by the SECSG human protein production group (T.A. Dailey, M. Mayer) under the direction of H.A. Dailey. Gene: TLP19 / Production host: Escherichia coli (E. coli) / References: UniProt: O95881 | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.74 % |
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Crystal grow | Temperature: 291 K / Method: modified batch crystallization / pH: 7 Details: 12% PEG 4000, 100mM Na Hepes, 100mM NaCl, pH 7.0, modified batch crystallization, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.07 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 19, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.199→38.633 Å / Num. all: 42206 / Num. obs: 42206 / Observed criterion σ(I): -3 |
-Phasing
Phasing | Method: MIR | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.53 / FOM acentric: 0.51 / FOM centric: 0.6 / Reflection: 7438 / Reflection acentric: 6336 / Reflection centric: 1102 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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Phasing MIR | Resolution: 2.5→20 Å / FOM: 0.33 / Reflection: 5250 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MIR shell |
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-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.199→38.633 Å / Cor.coef. Fo:Fc: 0.965 / SU R Cruickshank DPI: 0.041 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.564 Å2
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Refinement step | Cycle: LAST / Resolution: 1.199→38.633 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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