+Open data
-Basic information
Entry | Database: PDB / ID: 6lrw | |||||||||
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Title | Marsupenaeus japonicus ferritin mutant(T158H) pH 7.0 | |||||||||
Components | Ferritin | |||||||||
Keywords | METAL BINDING PROTEIN / ferroxidase / iron | |||||||||
Function / homology | Function and homology information ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis Similarity search - Function | |||||||||
Biological species | Penaeus japonicus (crustacean) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Zhao, G. / Tan, X. / Zhang, T. | |||||||||
Funding support | China, 2items
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Citation | Journal: Commun Chem / Year: 2020 Title: Converting histidine-induced 3D protein arrays in crystals into their 3D analogues in solution by metal coordination cross-linking. Authors: Tan, X. / Chen, H. / Gu, C. / Zhang, J. / Zhang, T. / Wang, H. / Zhao, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lrw.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lrw.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lrw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/6lrw ftp://data.pdbj.org/pub/pdb/validation_reports/lr/6lrw | HTTPS FTP |
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-Related structure data
Related structure data | 6lruC 6lrvC 6lrxC 6ls2C 6a4uS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19527.873 Da / Num. of mol.: 2 / Mutation: T158H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: T2B7E1, ferroxidase #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: 3.43 Å3/Da / Density % sol: 64.11 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2500 mM NaCl, 100 mM KH2PO3 / KH2PO3 (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 273.15 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→117.11 Å / Num. obs: 21207 / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.033 / Rrim(I) all: 0.146 / Χ2: 0.554 / Net I/σ(I): 3.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6a4u Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.233 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.209 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.35 Å2 / Biso mean: 23.269 Å2 / Biso min: 4.61 Å2
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Refinement step | Cycle: final / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.402→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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