+Open data
-Basic information
Entry | Database: PDB / ID: 6y2z | ||||||
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Title | NG domain of human SRP54 | ||||||
Components | Signal recognition particle 54 kDa protein | ||||||
Keywords | RNA BINDING PROTEIN / SRP54 NG domain / Protein translocation | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Juaire, K.D. / Wild, K. / Sinning, I. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Structure / Year: 2021 Title: Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia. Authors: Juaire, K.D. / Lapouge, K. / Becker, M.M.M. / Kotova, I. / Michelhans, M. / Carapito, R. / Wild, K. / Bahram, S. / Sinning, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y2z.cif.gz | 251.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y2z.ent.gz | 203.1 KB | Display | PDB format |
PDBx/mmJSON format | 6y2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y2z_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 6y2z_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 6y2z_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 6y2z_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/6y2z ftp://data.pdbj.org/pub/pdb/validation_reports/y2/6y2z | HTTPS FTP |
-Related structure data
Related structure data | 6y30C 6y31C 6y32C 5l3qS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33373.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SRP54 / Production host: Escherichia coli (E. coli) / References: UniProt: P61011 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.82 Å3/Da / Density % sol: 56.45 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: na2hpo4 0.8 M K2HPO4 0.8 M HEPES 0.1 M (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→48.371 Å / Num. obs: 42073 / % possible obs: 99.91 % / Redundancy: 13.2 % / Rpim(I) all: 0.056 / Net I/σ(I): 10.75 |
Reflection shell | Resolution: 2.15→2.23 Å / Num. unique obs: 4140 / Rsym value: 0.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L3Q Resolution: 2.15→48.371 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.66 Å2 / Biso mean: 53.335 Å2 / Biso min: 21.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→48.371 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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