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Yorodumi- PDB-4m1v: Crystal structure of the ancestral soluble variant of the Human P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m1v | ||||||
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Title | Crystal structure of the ancestral soluble variant of the Human Phosphate Binding Protein (HPBP) | ||||||
Components | Phosphate-binding protein | ||||||
Keywords | PROTEIN BINDING / phosphate-binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | unidentified prokaryotic organism (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Gonzalez, D. / Hiblot, J. / Darbinian, N. / Miller, J.S. / Gotthard, G. / Amini, S. / Chabriere, E. / Elias, M. | ||||||
Citation | Journal: FEBS Open Bio / Year: 2014 Title: Ancestral mutations as a tool for solubilizing proteins: The case of a hydrophobic phosphate-binding protein. Authors: Gonzalez, D. / Hiblot, J. / Darbinian, N. / Miller, J.C. / Gotthard, G. / Amini, S. / Chabriere, E. / Elias, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m1v.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m1v.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 4m1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m1v_validation.pdf.gz | 470.4 KB | Display | wwPDB validaton report |
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Full document | 4m1v_full_validation.pdf.gz | 474.3 KB | Display | |
Data in XML | 4m1v_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 4m1v_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/4m1v ftp://data.pdbj.org/pub/pdb/validation_reports/m1/4m1v | HTTPS FTP |
-Related structure data
Related structure data | 2v3qS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39002.320 Da / Num. of mol.: 1 Mutation: L15Q; I37A; A70S; A74S; G79T; A102T; A121T; A129S; A141S; P162T; L177G; L182T; D192Q; A196T; I211M; V237A; L261V; G268T; G283A; G314T; A328N; V350I Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified prokaryotic organism (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: P85173 |
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-Non-polymers , 5 types, 659 molecules
#2: Chemical | ChemComp-PO4 / | ||||
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#3: Chemical | ChemComp-ACT / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / | #6: 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: 2.19 Å3/Da / Density % sol: 43.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: The protein was concentrated at 4mg/mL. The conditions are 0.2M sodium acetate, 0.1M sodium cacodylate, 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97655 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97655 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→99.9103 Å / Num. all: 268471 / Num. obs: 81625 / % possible obs: 98.8 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 21.36 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 3.23 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4.65 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2V3Q Resolution: 1.3→36.1 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.368 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.996 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→36.1 Å
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Refine LS restraints |
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