+Open data
-Basic information
Entry | Database: PDB / ID: 3byp | ||||||
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Title | Mode of Action of a Putative Zinc Transporter CzrB | ||||||
Components | CzrB protein | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein / zinc transporter | ||||||
Function / homology | Function and homology information monoatomic cation transmembrane transporter activity / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Cherezov, V. / Srinivasan, V. / Szebenyi, D.M.E. / Caffrey, M. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Insights into the Mode of Action of a Putative Zinc Transporter CzrB in Thermus thermophilus Authors: Cherezov, V. / Hofer, N. / Szebenyi, D.M. / Kolaj, O. / Wall, J.G. / Gillilan, R. / Srinivasan, V. / Jaroniec, C.P. / Caffrey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3byp.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3byp.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 3byp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3byp_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 3byp_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 3byp_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 3byp_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/3byp ftp://data.pdbj.org/pub/pdb/validation_reports/by/3byp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10780.223 Da / Num. of mol.: 2 / Fragment: sequence database residues 198-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: czrB / Plasmid: pIVEX2.4d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8VLX7 #2: Chemical | #3: 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: 2.25 Å3/Da / Density % sol: 45.21 % |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: Protein solution 15 mg/ml protein, 20mM Tris, pH 8.0; precipitant solution 0.2M ammonium sulfate, 15% PEG 4000, 0.1M sodium acetate, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9124 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2006 |
Radiation | Monochromator: BENT SINGLE-CRYSTAL SI(111), WITH FOCUSING MIRROR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9124 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 21179 / % possible obs: 98.9 % / Redundancy: 12.8 % / Rsym value: 0.042 / Net I/σ(I): 54.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.393 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CZRB WITH ZN BOUND Resolution: 1.7→30.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.791 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 2 TLS GROUPS USED
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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: 28.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 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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