+Open data
-Basic information
Entry | Database: PDB / ID: 4xzs | |||||||||
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Title | Crystal Structure of TRIAP1-MBP fusion | |||||||||
Components | Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1 | |||||||||
Keywords | APOPTOSIS / lipid / cX9cX motif / cancer / mitochondria / chaperone | |||||||||
Function / homology | Function and homology information regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / phospholipid transport / phospholipid translocation / detection of maltose stimulus / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose transport complex / negative regulation of release of cytochrome c from mitochondria / maltose binding ...regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / phospholipid transport / phospholipid translocation / detection of maltose stimulus / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose transport complex / negative regulation of release of cytochrome c from mitochondria / maltose binding / maltose transport / maltodextrin transmembrane transport / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / carbohydrate transport / carbohydrate transmembrane transporter activity / DNA damage response, signal transduction by p53 class mediator / Mitochondrial protein degradation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / mitochondrial intermembrane space / cellular response to UV / p53 binding / outer membrane-bounded periplasmic space / periplasmic space / apoptotic process / DNA damage response / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | |||||||||
Authors | Miliara, X. / Garnett, J.A. / Abid-Ali, F. / Perez-Dorado, I. / Matthews, S.J. | |||||||||
Citation | Journal: Embo Rep. / Year: 2015 Title: Structural insight into the TRIAP1/PRELI-like domain family of mitochondrial phospholipid transfer complexes. Authors: Miliara, X. / Garnett, J.A. / Tatsuta, T. / Abid Ali, F. / Baldie, H. / Perez-Dorado, I. / Simpson, P. / Yague, E. / Langer, T. / Matthews, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xzs.cif.gz | 333.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xzs.ent.gz | 271.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/4xzs ftp://data.pdbj.org/pub/pdb/validation_reports/xz/4xzs | HTTPS FTP |
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-Related structure data
Related structure data | 4xzvC 1hsjS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 1 - 419 / Label seq-ID: 2 - 420
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-Components
#1: Protein | Mass: 48939.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human) Gene: malE, b4034, JW3994, TRIAP1, 15E1.1, HSPC132 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: O43715 #2: Polysaccharide | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 100 mM sodium acetate, 25% (w/v) PEG 4000, 18% (w/v) MPD, 200 mM ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→48.41 Å / Num. obs: 45307 / % possible obs: 98.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.12→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.2 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1hsj Resolution: 2.12→48.41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 42.257 Å2
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Refinement step | Cycle: 1 / Resolution: 2.12→48.41 Å
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Refine LS restraints |
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