+Open data
-Basic information
Entry | Database: PDB / ID: 2j45 | ||||||
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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 / NUCLEOTIDE-BINDING / 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 | 2j45.cif.gz | 657.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j45.ent.gz | 561.5 KB | Display | PDB format |
PDBx/mmJSON format | 2j45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/2j45 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/2j45 | HTTPS FTP |
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-Related structure data
Related structure data | 2j46C 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: (-0.837332, 0.022351, 0.546238), 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 , 6 types, 909 molecules
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
-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 % Description: DATA WERE COLLECTED IN THREE OVERLAPPING RESOLUTION PASSES |
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Crystal grow | pH: 6.1 / Details: 30% MPD, 100MM MES, PH 6.1, 20MM CACL2, 2MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 23, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→30 Å / Num. obs: 195214 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.14→1.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4 / % possible all: 88.8 |
-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: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.008 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: NO WATER HYDROGEN ATOMS ARE 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: 16.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→29.84 Å
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Refine LS restraints |
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