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Yorodumi- PDB-4f3p: Crystal structure of a Glutamine-binding periplasmic protein from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f3p | ||||||
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Title | Crystal structure of a Glutamine-binding periplasmic protein from Burkholderia pseudomallei in complex with glutamine | ||||||
Components | Glutamine-binding periplasmic protein | ||||||
Keywords | TRANSPORT PROTEIN / SSGCID / Structural genomics / Burkholderia pseudomallei / glutamine / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a Glutamine-binding periplasmic protein from Burkholderia pseudomallei in complex with glutamine Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Fairman, J.W. / Staker, B. / Myler, P. / Stewart, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f3p.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f3p.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 4f3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/4f3p ftp://data.pdbj.org/pub/pdb/validation_reports/f3/4f3p | HTTPS FTP |
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-Related structure data
Related structure data | 1gggS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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 domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 26 - 244 / Label seq-ID: 24 - 242
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-Components
#1: Protein | Mass: 27333.207 Da / Num. of mol.: 2 / Fragment: unp residues 25-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_A1487, glnH / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JIF9 #2: 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: 2.27 Å3/Da / Density % sol: 45.83 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MD Morpheus screen C12: 12.5% PEG 3350, 12.5% PEG 1000, 12.5% MPD, 30mM sodium nitrate, 30mM disodium hydrgon phosphate, 30mM ammonium sulphate, 100mM bicine/trizma; BupsA.17285.b.A2 PW ...Details: MD Morpheus screen C12: 12.5% PEG 3350, 12.5% PEG 1000, 12.5% MPD, 30mM sodium nitrate, 30mM disodium hydrgon phosphate, 30mM ammonium sulphate, 100mM bicine/trizma; BupsA.17285.b.A2 PW PS01148 20mg/ml, tray 232242c12, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ASYMMETRIC CURVED CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. all: 19275 / Num. obs: 19249 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37.414 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.36 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1ggg modified with CCP4 program chainsaw Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.1849 / WRfactor Rwork: 0.1519 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.864 / SU B: 13.829 / SU ML: 0.164 / SU R Cruickshank DPI: 0.3878 / SU Rfree: 0.2297 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 71.14 Å2 / Biso mean: 30.518 Å2 / Biso min: 10.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 7249 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.09 / Type: LOCAL / Weight: 0.05
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LS refinement shell | Resolution: 2.4→2.462 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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