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Yorodumi- PDB-1qb2: CRYSTAL STRUCTURE OF THE CONSERVED SUBDOMAIN OF HUMAN PROTEIN SRP... -
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-Basic information
Entry | Database: PDB / ID: 1qb2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE CONSERVED SUBDOMAIN OF HUMAN PROTEIN SRP54M AT 2.1A RESOLUTION: EVIDENCE FOR THE MECHANISM OF SIGNAL PEPTIDE BINDING | ||||||
Components | HUMAN SIGNAL RECOGNITION PARTICLE 54 KD PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / ALPHA-HELIX / HELIX-TURN-HELIX | ||||||
Function / homology | Function and homology information SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation ...SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / neutrophil chemotaxis / GDP binding / nuclear speck / GTPase activity / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Clemons Jr., W.M. / Gowda, K. / Black, S.D. / Zwieb, C. / Ramakrishnan, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of the conserved subdomain of human protein SRP54M at 2.1 A resolution: evidence for the mechanism of signal peptide binding. Authors: Clemons Jr., W.M. / Gowda, K. / Black, S.D. / Zwieb, C. / Ramakrishnan, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qb2.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qb2.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qb2_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 1qb2_full_validation.pdf.gz | 450.2 KB | Display | |
Data in XML | 1qb2_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1qb2_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/1qb2 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/1qb2 | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 12473.440 Da / Num. of mol.: 2 / Fragment: SRP54 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: PLACENTA / Description: T7 BASED EXPRESSION SYSTEM / Cellular location: CYTOPLASM / Organ: PLACENTA / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / Keywords: FRAGMENT, CONSERVED M DOMAIN / References: UniProt: P61011 #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: 2.3 Å3/Da / Density % sol: 46.42 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG 2K, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. all: 25000 / Num. obs: 25000 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.057 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.296 / % possible all: 94 | |||||||||||||||||||||||||
Reflection | *PLUS % possible obs: 99 % / Num. measured all: 165944 | |||||||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 94 % / Mean I/σ(I) obs: 2.6 |
-Processing
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Refinement | Resolution: 2.1→50 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 50 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d |