+Open data
-Basic information
Entry | Database: PDB / ID: 2j46 | ||||||
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Title | Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution | ||||||
Components | SIGNAL RECOGNITION PARTICLE PROTEIN | ||||||
Keywords | NUCLEOTIDE-BINDING / RIBONUCLEOPROTEIN / SRP / FFH / WATER / GTPASE / RNA-BINDING / GTP-BINDING / SIGNAL RECOGNITION PARTICLE | ||||||
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: 1.14 Å | ||||||
Authors | Freymann, D.M. / Ramirez, U.D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Analysis of Protein Hydration in Ultra-High Resolution Structures of the Srp Gtpase Ffh Authors: Ramirez, U.D. / Freymann, D.M. #1: Journal: J.Mol.Biol. / Year: 2002 Title: Structural Basis for Mobility in the 1.1A Crystal Structure of the Ng Domain of T. Aquaticus Ffh Authors: Ramirez, U.D. / Minasov, G. / Focia, P.J. / Stroud, R. / Walter, P. / Kuhn, P. / 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 | 2j46.cif.gz | 529.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j46.ent.gz | 444.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/2j46 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/2j46 | HTTPS FTP |
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-Related structure data
Related structure data | 2j45C 1jpnS 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: (-0.80778, 0.054302, 0.586977), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32571.637 Da / Num. of mol.: 2 / Fragment: G DOMAIN, 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 |
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-Non-polymers , 5 types, 569 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: 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: 45.3 % |
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Crystal grow | pH: 4.7 Details: 30% MPD, 0.1M NAACETATE, PH 4.7, 0.1M MNCL2, 2MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.785 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.785 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→18.5 Å / Num. obs: 199458 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.1→1.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.6 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JPN Resolution: 1.14→29.84 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.163 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: NO WATER HYDROGEN ATOMS ARE INCLUDED I INCLUDED IN THESE COORDINATES
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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: 21.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→29.84 Å
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Refine LS restraints |
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