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Yorodumi- PDB-3n5l: Crystal structure of a binding protein component of ABC phosphona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n5l | ||||||
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Title | Crystal structure of a binding protein component of ABC phosphonate transporter (PA3383) from Pseudomonas aeruginosa at 1.97 A resolution | ||||||
Components | Binding protein component of ABC phosphonate transporter | ||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / ABC transport system / periplasmic phosphonate-binding | ||||||
Function / homology | Function and homology information organic phosphonate transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.97 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a binding protein component of ABC phosphonate transporter (PA3383) from Pseudomonas aeruginosa at 1.97 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n5l.cif.gz | 269.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n5l.ent.gz | 220.9 KB | Display | PDB format |
PDBx/mmJSON format | 3n5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/3n5l ftp://data.pdbj.org/pub/pdb/validation_reports/n5/3n5l | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34867.328 Da / Num. of mol.: 2 / Fragment: sequence database residues 26-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3383 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HYL8 |
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-Non-polymers , 5 types, 667 molecules
#2: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | (1) THE CONSTRUCT (RESIDUES 26-334) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...(1) THE CONSTRUCT (RESIDUES 26-334) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI |
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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: 3.46 Å3/Da / Density % sol: 64.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.000000000M (NH4)2SO4, 0.200000000M Li2SO4, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2010 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.97→49.445 Å / Num. obs: 68965 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.138 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.37 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.97→49.445 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.02 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.113 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A UNKNOWN LIGAND (UNL), RESEMBLING GLYCEROL-3-PHOSPHATE WAS MODELED INTO THE BINDING SITE OF EACH MONOMER. THE PROTEIN IS A HOMOLOG OF PHND OF E. COLI, WHICH BINDS ALKYLPHOSPHONATE. ETHYLENE GLYCOL (EDO), SULFATE (SO4) AND CHLORIDE (CL) MODELED ARE PRESENT PROTEIN/CRYSTALLIZATION/CRYO BUFFER.
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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 max: 130.02 Å2 / Biso mean: 30.65 Å2 / Biso min: 11.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→49.445 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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