+Open data
-Basic information
Entry | Database: PDB / ID: 7fbd | ||||||
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Title | De novo design protein D53 with MBP tag | ||||||
Components | Maltodextrin-binding protein,De novo design protein D53 | ||||||
Keywords | UNKNOWN FUNCTION / DE NOVO PROTEIN | ||||||
Function / homology | Function and homology information carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space Similarity search - Function | ||||||
Biological species | Serratia sp. (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.85 Å | ||||||
Authors | Bin, H. | ||||||
Funding support | 1items
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Citation | Journal: Nature / Year: 2022 Title: A backbone-centred energy function of neural networks for protein design. Authors: Huang, B. / Xu, Y. / Hu, X. / Liu, Y. / Liao, S. / Zhang, J. / Huang, C. / Hong, J. / Chen, Q. / Liu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fbd.cif.gz | 337.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fbd.ent.gz | 278 KB | Display | PDB format |
PDBx/mmJSON format | 7fbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fbd_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 7fbd_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 7fbd_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 7fbd_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/7fbd ftp://data.pdbj.org/pub/pdb/validation_reports/fb/7fbd | HTTPS FTP |
-Related structure data
Related structure data | 7dguC 7dgwC 7dgyC 7dkkC 7dkoC 7dmfC 7fbbC 7fbcC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48712.336 Da / Num. of mol.: 2 / Mutation: D84A,K85A,E174A,N175A,K241A,E361A,K364A,D365A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia sp. (strain FS14) (bacteria), (gene. exp.) synthetic construct (others) Strain: FS14 / Gene: malE, JW3994 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P1LXE0 |
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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: 3.33 Å3/Da / Density % sol: 63.04 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.2M Sodium malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 18, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.605→89.03 Å / Num. obs: 29930 / % possible obs: 100 % / Redundancy: 16.8 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.506 / Rpim(I) all: 0.125 / Rrim(I) all: 0.522 / Net I/σ(I): 5.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.85→13.081 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.26 / Stereochemistry target values: ML Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.11 Å2 / Biso mean: 33.0972 Å2 / Biso min: 13.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→13.081 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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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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