+Open data
-Basic information
Entry | Database: PDB / ID: 2c03 | ||||||
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Title | GDP COMPLEX OF SRP GTPASE FFH NG DOMAIN | ||||||
Components | SIGNAL RECOGNITION PARTICLE PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / FFH / GMPPNP / GTP-BINDING / NG DOMAIN / RNA-BINDING / SRP54 NUCLEOTIDE-BINDING / SIGNAL PROTEIN | ||||||
Function / homology | Function and homology information signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity Similarity search - Function | ||||||
Biological species | THERMUS AQUATICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Ramirez, U.D. / Preininger, A.M. / Freymann, D.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Nucleotide-Binding Flexibility in Ultrahigh-Resolution Structures of the Srp Gtpase Ffh Authors: Ramirez, U.D. / Focia, P.J. / Freymann, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c03.cif.gz | 606.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c03.ent.gz | 512.4 KB | Display | PDB format |
PDBx/mmJSON format | 2c03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/2c03 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/2c03 | HTTPS FTP |
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-Related structure data
Related structure data | 2c04C 1ffhS 2bqs 2bqt 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 oper: (Code: given Matrix: (0.873394, 0.008997, -0.486931), Vector: |
-Components
#1: Protein | Mass: 32601.660 Da / Num. of mol.: 2 / Fragment: NG, RESIDUES 1-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O07347 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-DIO / #5: Water | ChemComp-HOH / | Compound details | MANDATORY FOR EFFICIENT EXPORT OF EXTRA-CYTOPLASMI | |
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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: 1.5 Å3/Da / Density % sol: 43.9 % Description: DATA WERE COLLECTED IN TWO OVERLAPPING RESOLUTION RANGES |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: 30% DIOXANE, 2MM GDP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.7429 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 14, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7429 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→50 Å / Num. obs: 154602 / % possible obs: 94.6 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.24→1.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FFH Resolution: 1.24→19.96 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.852 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.057 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→19.96 Å
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