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Open data
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Basic information
Entry | Database: PDB / ID: 2cnw | ||||||
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Title | GDPALF4 complex of the SRP GTPases Ffh and FtsY | ||||||
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![]() | SIGNAL RECOGNITION / INNER MEMBRANE / MEMBRANE TARGETING / NUCLEOTIDE-BINDING / GDP- ALUMINUM FLUORIDE / SIGNAL RECOGNITION PARTICLE / RNA-BINDING / GTP-BINDING / CELL DIVISION / SIGNAL SEQUENCE RECOGNITION / SRP / FFH / FTSY / GTPASE / MEMBRANE / CELL CYCLE / CELL DIVISION-COMPLEX | ||||||
Function / homology | ![]() endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / GTPase activity / GTP binding / ATP hydrolysis activity ...endoplasmic reticulum signal peptide binding / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Focia, P.J. / Gawronski-Salerno, J. / Coon V, J.S. / Freymann, D.M. | ||||||
![]() | ![]() Title: Structure of a Gdp:Alf(4) Complex of the Srp Gtpases Ffh and Ftsy, and Identification of a Peripheral Nucleotide Interaction Site. Authors: Focia, P.J. / Gawronski-Salerno, J. / Coon V, J.S. / Freymann, D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 354.3 KB | Display | ![]() |
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PDB format | ![]() | 284.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1okkS ![]() 2bqs ![]() 2bqt S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 32300.371 Da / Num. of mol.: 3 / Fragment: NG DOMAIN RESIDUES 1-293 Source method: isolated from a genetically manipulated source Details: GDP, ALF4, GMP / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 30764.586 Da / Num. of mol.: 3 / Fragment: RESIDUES 20-303 Source method: isolated from a genetically manipulated source Details: GDP, ALF4, GMP / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 642 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GDP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ALF / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE FIRST 19 RESIDUES PRESENT IN THE UNP ENTRY P83749 WERE DELETED IN CHAINS D, E AND F. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.23 % |
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Crystal grow | pH: 8.5 / Details: 0.1M TRIS-HCL (PH 8.5), 25% (W/V) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 18, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→14.9 Å / Num. obs: 287923 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.39→2.52 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OKK Resolution: 2.39→14.68 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.447 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THIRTY THREE GLUTAMATE SIDECHAINS A53, A150, A173, A174, A207, A285, B46, B53, B57, B84, B150, B174, B B285, C11, C57, C84, C150, C173, C196, C201, C207, C285, D99, D D245, E151, E165, E204, ...Details: THIRTY THREE GLUTAMATE SIDECHAINS A53, A150, A173, A174, A207, A285, B46, B53, B57, B84, B150, B174, B B285, C11, C57, C84, C150, C173, C196, C201, C207, C285, D99, D D245, E151, E165, E204, E245, F151, F165, F245 EXHIBIT EVIDENCE RADIATION DAMAGE AND THEIR CARBOXYLATE GROUP CD-OE1-OE2 ATOMS A MODELED AT 0.5 OCCUPANCY. ASPARTATE E79 ALSO EXHIBITS EVIDENCE RADIATION DAMAGE AND CARBOXYLATE GROUP ATOMS CG-OD1-OD2 ARE MOD AT 0.5 OCCUPANCY. WATERS THAT ARE IN CHAINS A, B, C, D, E AND F THE NUCLEOPHILIC AND METAL COORDINATING WATER MOLECULES.
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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: 35.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→14.68 Å
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Refine LS restraints |
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