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Yorodumi- PDB-1p32: CRYSTAL STRUCTURE OF HUMAN P32, A DOUGHNUT-SHAPED ACIDIC MITOCHON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p32 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN P32, A DOUGHNUT-SHAPED ACIDIC MITOCHONDRIAL MATRIX PROTEIN | ||||||
Components | MITOCHONDRIAL MATRIX PROTEIN, SF2P32 | ||||||
Keywords | MITOCHONDRIAL MATRIX PROTEIN | ||||||
Function / homology | Function and homology information adrenergic receptor binding / Apoptotic factor-mediated response / Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function / negative regulation of MDA-5 signaling pathway / kininogen binding / negative regulation of RIG-I signaling pathway / : / negative regulation of defense response to virus / positive regulation of dendritic cell chemotaxis / hyaluronic acid binding ...adrenergic receptor binding / Apoptotic factor-mediated response / Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function / negative regulation of MDA-5 signaling pathway / kininogen binding / negative regulation of RIG-I signaling pathway / : / negative regulation of defense response to virus / positive regulation of dendritic cell chemotaxis / hyaluronic acid binding / complement component C1q complex binding / translation activator activity / positive regulation of trophoblast cell migration / mitochondrial ribosome binding / blood coagulation, intrinsic pathway / regulation of complement activation / positive regulation of mitochondrial translation / negative regulation of interleukin-12 production / positive regulation of neutrophil chemotaxis / enzyme inhibitor activity / presynaptic active zone / RHOC GTPase cycle / negative regulation of mRNA splicing, via spliceosome / transcription factor binding / negative regulation of type II interferon production / positive regulation of cell adhesion / RHOA GTPase cycle / GABA-ergic synapse / negative regulation of double-strand break repair via homologous recombination / positive regulation of substrate adhesion-dependent cell spreading / Intrinsic Pathway of Fibrin Clot Formation / viral process / intrinsic apoptotic signaling pathway / complement activation, classical pathway / RNA splicing / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytosolic ribosome assembly / protein kinase C binding / mRNA processing / transcription corepressor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitochondrial matrix / immune response / positive regulation of apoptotic process / innate immune response / mRNA binding / glutamatergic synapse / apoptotic process / nucleolus / negative regulation of transcription by RNA polymerase II / cell surface / mitochondrion / extracellular space / extracellular region / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å | ||||||
Authors | Jiang, J. / Zhang, Y. / Krainer, A.R. / Xu, R.-M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Crystal structure of human p32, a doughnut-shaped acidic mitochondrial matrix protein. Authors: Jiang, J. / Zhang, Y. / Krainer, A.R. / Xu, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p32.cif.gz | 125.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p32.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 1p32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/1p32 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/1p32 | 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:
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-Components
#1: Protein | Mass: 23826.105 Da / Num. of mol.: 3 / Mutation: L74M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli / References: UniProt: MA32_HUMAN, UniProt: Q07021*PLUS #2: 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: 2.16 Å3/Da / Density % sol: 44.5 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95,0.9786,0.9789,1.0 | |||||||||||||||
Detector | Type: BRANDEIS / Detector: CCD / Date: Jan 1, 1998 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.25→50 Å / Num. obs: 27284 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.045 / Rsym value: 0.107 / Net I/σ(I): 15.4 | |||||||||||||||
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.139 / % possible all: 59.8 | |||||||||||||||
Reflection | *PLUS Num. measured all: 170171 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 59.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.25→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Details: INITIALLY THE MODEL WAS REFINED BY XPLOR
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Solvent computation | Solvent model: DENSITY MODIFICATION / Bsol: 56.0793 Å2 / ksol: 0.359245 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.33 Å
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Xplor file |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.1926 |