+Open data
-Basic information
Entry | Database: PDB / ID: 4fzo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the apo-form uranyl binding protein | ||||||
Components | uranyl binding protein | ||||||
Keywords | UNKNOWN FUNCTION / uranyl binding / uranyl | ||||||
Function / homology | Domain of unknown function DUF357 / AF1782-like superfamily / Protein of unknown function (DUF357) / AF1782-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha / DUF357 domain-containing protein Function and homology information | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | He, C. / Zhou, L. / Zhang, L. | ||||||
Citation | Journal: Nat Chem / Year: 2014 Title: A protein engineered to bind uranyl selectively and with femtomolar affinity. Authors: Zhou, L. / Bosscher, M. / Zhang, C. / Ozcubukcu, S. / Zhang, L. / Zhang, W. / Li, C.J. / Liu, J. / Jensen, M.P. / Lai, L. / He, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4fzo.cif.gz | 48.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4fzo.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fzo_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4fzo_full_validation.pdf.gz | 431.6 KB | Display | |
Data in XML | 4fzo_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 4fzo_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/4fzo ftp://data.pdbj.org/pub/pdb/validation_reports/fz/4fzo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9542.686 Da / Num. of mol.: 2 / Mutation: L13D, D17E, H64E, L67T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: MTH_1690 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / References: UniProt: O27725 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 31.07 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 3350, Tacsimate 4.0, sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→38.2 Å / Num. all: 34522 / Num. obs: 34522 / % possible obs: 15.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 7.69 Å2 |
Reflection shell | Resolution: 1.3→1.35 Å / % possible all: 89.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→38.193 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.11 / σ(F): 1.39 / Phase error: 15.85 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.305 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→38.193 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|