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Yorodumi- PDB-2j7p: GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j7p | ||||||
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Title | GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY | ||||||
Components |
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Keywords | SIGNAL RECOGNITION / INNER MEMBRANE / MEMBRANE TARGETING / NUCLEOTIDE-BINDING / GMPPNP / GDP-PNP / SIGNAL RECOGNITION PARTICLE / RNA-BINDING / GTP-BINDING / CELL DIVISION / SIGNAL SEQUENCE RECOGNITION / SRP / FFH / FTSY / GTPASE / MEMBRANE / CELL CYCLE / CELL DIVISION-COMPLEX | ||||||
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 / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | THERMUS AQUATICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Freymann, D.M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2007 Title: Structure of the Gmppnp-Stabilized Ng Domain Complex of the Srp Gtpases Ffh and Ftsy. Authors: Gawronski-Salerno, 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 | 2j7p.cif.gz | 243.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j7p.ent.gz | 193.1 KB | Display | PDB format |
PDBx/mmJSON format | 2j7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/2j7p ftp://data.pdbj.org/pub/pdb/validation_reports/j7/2j7p | HTTPS FTP |
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-Related structure data
Related structure data | 1okkS S: Starting model for refinement |
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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:
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-Components
-Protein , 2 types, 4 molecules ABDE
#1: Protein | Mass: 32300.371 Da / Num. of mol.: 2 / Fragment: NG, RESIDUES 1-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O07347 #2: Protein | Mass: 30693.510 Da / Num. of mol.: 2 / Fragment: NG, RESIDUES 21-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83749 |
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-Non-polymers , 6 types, 586 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-GNP / #6: Chemical | ChemComp-MG / #7: Chemical | #8: 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: 2.24 Å3/Da / Density % sol: 44.71 % |
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Crystal grow | pH: 7.5 / Details: 0.2 M KI, 20% PEG 3350, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.011289 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.011289 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 79821 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.8 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OKK Resolution: 1.97→19.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.251 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.168 / 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: 29.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→19.94 Å
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Refine LS restraints |
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