+Open data
-Basic information
Entry | Database: PDB / ID: 6n01 | ||||||
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Title | Structure of apo AztD from Citrobacter koseri | ||||||
Components | AztD Protein | ||||||
Keywords | CHAPERONE / periplasm / beta propeller / zinc / metallochaperone | ||||||
Function / homology | Nitrous oxide reductase, N-terminal / WD40/YVTN repeat-like-containing domain superfamily / TRIETHYLENE GLYCOL / YncE family protein Function and homology information | ||||||
Biological species | Citrobacter koseri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Yukl, E.T. / Neupane, D.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2019 Title: Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins. Authors: Neupane, D.P. / Fullam, S.H. / Chacon, K.N. / Yukl, E.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n01.cif.gz | 523.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n01.ent.gz | 433.8 KB | Display | PDB format |
PDBx/mmJSON format | 6n01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n01_validation.pdf.gz | 489.7 KB | Display | wwPDB validaton report |
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Full document | 6n01_full_validation.pdf.gz | 504.2 KB | Display | |
Data in XML | 6n01_validation.xml.gz | 55.6 KB | Display | |
Data in CIF | 6n01_validation.cif.gz | 78.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/6n01 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/6n01 | HTTPS FTP |
-Related structure data
Related structure data | 6ck1C 6cmkSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 45467.371 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) (bacteria) Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / Gene: CKO_00948 / Production host: Escherichia coli (E. coli) / References: UniProt: A8AF35 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MES / | #5: 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: 45.45 % |
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Crystal grow | Temperature: 292 K / Method: batch mode / pH: 6 Details: 10 mg/mL protein was combined in a 1:1 ratio with 24% PEG 4000, 0.1 M sodium nitrate, 0.1 M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2018 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→48.43 Å / Num. obs: 110365 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Χ2: 0.9 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 16782 / CC1/2: 0.758 / Rpim(I) all: 0.326 / Rrim(I) all: 0.621 / Χ2: 0.69 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6cmk Resolution: 1.98→48.431 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→48.431 Å
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Refine LS restraints |
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LS refinement shell |
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